genome.fa.s6.2.7.7.80.10.50.1000.28.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  28  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)
7389794--7389937	38	3.9	37	76	14	147	36	29	21	13	1.91
7389869--7389929	16	3.8	16	91	0	104	34	31	22	11	1.90
7390509--7390549	19	2.2	19	100	0	82	14	24	19	41	1.89
7394566--7394617	18	2.9	18	91	0	86	38	23	23	15	1.92
7407213--7407257	18	2.5	18	78	7	56	42	17	2	37	1.62
7408197--7408231	17	2.0	18	88	5	54	11	42	31	14	1.81
7412480--7412535	21	2.7	21	88	0	85	26	8	35	28	1.87
7425117--7425154	17	2.2	17	86	9	51	57	5	10	26	1.53
7430352--7430432	40	2.0	40	100	0	162	40	12	19	27	1.87
7431518--7431575	2	30.0	2	80	19	70	50	0	3	46	1.18
7431613--7431649	18	2.2	18	86	13	53	67	0	10	21	1.21
7433101--7433174	25	3.0	25	95	0	130	21	27	20	31	1.98
7433103--7433192	25	3.6	25	89	3	101	25	26	20	27	1.99
7437816--7437877	26	2.4	26	86	0	88	35	9	17	37	1.83
7441655--7441712	16	3.6	16	75	9	55	32	3	3	60	1.30
7443667--7443708	19	2.3	18	88	8	59	19	14	7	59	1.57
7443851--7443900	26	1.9	26	95	0	91	20	20	4	56	1.58
7444020--7444087	9	7.3	9	78	18	77	22	1	1	75	0.97
7444012--7444087	19	4.1	17	77	15	80	22	1	1	75	0.96
7444019--7444095	18	4.2	18	77	6	64	27	1	1	70	1.03
7447986--7448029	15	2.8	16	82	10	54	47	9	9	34	1.67
7451628--7451688	31	2.0	29	84	12	79	34	9	1	54	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7451721--7451802	4	20.5	4	100	0	164	50	24	0	25	1.50
7451789--7451855	27	2.4	28	80	9	84	41	10	1	46	1.47
7452006--7452050	22	2.0	22	100	0	90	33	4	13	48	1.62
7452355--7452497	73	1.9	74	92	4	245	27	18	16	36	1.93
7455408--7455441	13	2.8	12	86	8	50	85	0	14	0	0.60
7456823--7457437	132	4.7	132	87	0	838	29	19	24	25	1.99
7457537--7457688	51	3.0	51	80	0	178	28	17	26	26	1.98
7457709--7457835	44	2.8	45	78	8	143	29	18	22	29	1.97
7458025--7458192	44	3.8	44	80	9	180	30	22	20	27	1.98
7457982--7458218	44	5.3	44	75	10	171	30	20	21	27	1.98
7458268--7458367	51	2.0	51	85	0	137	31	19	24	26	1.98
7457848--7458615	404	1.9	403	90	0	1221	31	19	21	27	1.97
7458383--7458599	45	4.9	45	73	6	163	30	20	21	27	1.98
7458429--7458639	44	4.8	44	70	6	140	31	18	19	29	1.96
7458712--7459013	138	2.2	135	86	2	408	30	20	19	29	1.97
7458712--7459049	138	2.5	138	83	2	387	31	21	18	28	1.97
7460480--7460540	31	2.0	29	84	12	79	34	9	1	54	1.44
7460579--7460642	27	2.3	27	86	2	83	40	9	1	48	1.45
7460637--7460759	2	61.5	2	72	6	79	43	9	0	46	1.42
7460601--7460759	38	4.3	37	77	12	148	42	8	0	48	1.39
7461131--7461272	72	2.0	72	90	0	221	29	19	16	34	1.94
7464842--7464916	31	2.4	31	84	4	89	32	12	10	45	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7471915--7471952	2	19.5	2	94	5	69	50	0	0	50	1.00
7472567--7472615	23	2.0	23	84	7	62	16	2	26	55	1.52
7472675--7472716	20	2.1	20	86	0	57	28	4	2	64	1.26
7472680--7472723	20	2.2	20	83	0	52	31	4	2	61	1.28
7472738--7472780	18	2.4	16	79	20	50	39	0	11	48	1.40
7472967--7473031	11	5.9	11	73	7	60	43	1	32	23	1.63
7472954--7473031	22	3.7	21	76	6	68	42	2	32	23	1.67
7480595--7480634	19	2.1	19	100	0	80	20	5	37	37	1.74
7487270--7487303	11	2.9	12	91	8	61	52	17	20	8	1.71
7489742--7489804	25	2.6	25	80	7	67	41	22	20	15	1.90
7491609--7491711	3	34.3	3	84	7	138	31	1	1	65	1.15
7491858--7491912	2	29.0	2	76	10	53	45	0	1	52	1.11
7492208--7492511	109	2.8	109	89	1	461	31	18	17	33	1.94
7493840--7494225	192	2.0	192	100	0	772	34	17	13	34	1.89
7496344--7496423	42	1.9	42	100	0	160	51	20	12	16	1.76
7497063--7497111	17	2.9	17	82	14	66	79	0	20	0	0.73
7497059--7497105	21	2.3	20	85	3	58	82	0	17	0	0.66
7497059--7497112	20	2.9	17	76	23	56	81	0	18	0	0.69
7497702--7498099	44	9.0	44	80	4	415	28	25	23	21	1.99
7497702--7498099	89	4.5	88	85	2	415	28	25	23	21	1.99
7497702--7498030	133	2.5	133	92	1	534	27	25	23	23	2.00
7497703--7498099	133	3.0	133	88	2	485	28	25	23	21	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7498264--7498312	24	2.0	24	96	0	89	24	24	26	24	2.00
7499699--7499739	9	4.6	9	90	6	57	24	0	0	75	0.80
7499696--7499762	18	3.9	18	81	12	63	26	2	1	68	1.12
7499697--7499733	15	2.4	15	95	4	65	21	0	0	78	0.75
7499906--7499970	2	34.0	2	80	9	64	44	0	1	53	1.09
7500272--7500577	109	2.8	109	87	3	433	31	17	17	33	1.94
7502199--7502250	19	2.9	17	82	8	59	25	0	1	73	0.94
7502199--7502250	18	2.8	19	75	16	56	25	0	1	73	0.94
7507123--7507505	50	7.9	49	81	7	349	26	20	21	31	1.98
7507164--7507505	140	2.4	145	86	6	455	26	21	21	29	1.99
7507489--7508433	88	10.7	88	92	1	1412	26	24	22	27	2.00
7509535--7509578	21	2.1	21	86	0	61	25	38	11	25	1.89
7509665--7509717	23	2.3	23	83	6	63	13	15	0	71	1.14
7509667--7509719	15	3.4	15	82	15	63	11	13	0	75	1.05
7510553--7510603	9	5.6	9	88	9	68	5	0	5	88	0.64
7510553--7510587	10	3.6	10	92	3	54	8	0	2	88	0.61
7510554--7510604	26	2.0	26	85	14	63	5	0	7	86	0.71
7510548--7510605	9	6.5	10	83	16	67	8	0	8	82	0.84
7514924--7514967	2	22.0	2	85	0	61	45	0	6	47	1.29
7515073--7515113	22	1.9	21	90	5	64	51	0	4	43	1.23
7516815--7516847	15	2.2	15	100	0	66	39	6	18	36	1.75
7523267--7523317	22	2.3	23	80	12	63	66	3	9	19	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7523413--7523462	24	2.1	24	84	0	64	46	6	26	22	1.74
7534020--7534105	40	2.2	40	91	0	145	44	17	5	32	1.73
7536071--7536172	18	5.8	18	69	16	63	59	0	1	37	1.15
7537180--7537206	13	2.1	13	100	0	54	37	0	14	48	1.45
7550962--7551013	22	2.4	22	100	0	104	21	21	28	28	1.98
7552350--7552375	5	5.2	5	100	0	52	19	19	19	42	1.90
7552866--7552905	20	2.0	20	90	0	62	40	5	17	37	1.72
7558908--7558966	26	2.3	26	87	0	82	30	13	15	40	1.86
7568145--7568173	13	2.3	13	94	5	51	6	0	6	86	0.72
7569622--7569721	49	2.0	49	96	0	182	47	10	10	33	1.70
7577315--7577401	44	2.0	45	84	6	115	51	2	10	35	1.49
7582633--7583229	300	2.0	298	88	2	885	25	19	16	39	1.91
7583610--7583638	13	2.2	13	100	0	58	10	27	13	48	1.75
7596195--7596248	2	27.0	2	100	0	108	50	0	0	50	1.00
7597541--7597578	20	1.9	20	94	0	67	52	2	0	44	1.14
7602080--7602113	2	17.0	2	100	0	68	50	0	0	50	1.00
7603276--7603391	36	3.2	36	75	2	117	29	20	13	36	1.91
7614638--7614719	30	2.7	30	79	5	85	48	8	7	35	1.61
7614648--7614719	31	2.4	29	76	6	72	47	9	6	36	1.64
7615317--7615356	16	2.5	16	79	0	53	17	0	27	55	1.43
7615328--7615364	18	2.2	16	90	9	56	16	0	27	56	1.40
7615902--7615964	21	3.0	21	97	2	117	47	9	4	38	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7616598--7616730	41	3.2	41	93	2	214	27	24	21	27	1.99
7617006--7617093	2	44.0	2	100	0	176	50	0	0	50	1.00
7619210--7619620	125	3.3	125	94	0	716	27	17	23	31	1.97
7624611--7624723	28	4.0	28	96	0	199	30	25	11	31	1.91
7626054--7626086	12	2.5	13	85	14	50	12	0	15	72	1.12
7626054--7626087	13	2.7	12	90	9	50	11	0	14	73	1.10
7627550--7627922	43	8.8	42	83	7	319	28	31	18	21	1.97
7627593--7627898	86	3.6	85	87	3	411	27	33	16	21	1.96
7634256--7634294	7	5.6	7	87	0	60	33	51	0	15	1.44
7634248--7634295	21	2.3	21	88	0	78	31	47	0	20	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