genome.fa.s3.2.7.7.80.10.50.1000.44.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  44  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)
12394528--12394574	24	2.0	24	91	0	76	55	4	8	31	1.49
12395199--12395292	19	4.8	19	92	5	161	35	15	11	37	1.85
12395192--12395292	40	2.7	38	89	8	161	35	15	10	37	1.83
12406748--12406780	14	2.2	16	89	10	52	57	0	42	0	0.98
12408875--12408911	15	2.5	15	100	0	74	27	45	5	21	1.73
12422710--12422740	9	3.4	9	90	0	53	25	12	22	38	1.90
12422793--12422829	9	4.1	9	92	0	65	45	13	10	29	1.77
12423857--12423882	5	5.2	5	100	0	52	19	19	19	42	1.90
12429331--12429385	26	2.1	27	86	3	76	23	3	10	61	1.44
12430831--12430930	28	3.3	32	73	17	113	22	19	13	46	1.83
12430918--12430944	13	2.1	13	100	0	54	22	25	14	37	1.93
12430923--12431008	28	2.9	29	77	6	93	25	17	13	43	1.86
12431151--12431284	31	4.4	31	69	12	98	42	12	18	26	1.86
12431528--12431579	26	2.0	26	85	7	70	51	5	3	38	1.44
12448937--12448981	23	2.0	23	82	8	56	33	4	11	51	1.58
12449029--12449059	2	15.5	2	100	0	62	0	0	48	51	1.00
12449403--12449441	2	19.5	2	100	0	78	48	0	0	51	1.00
12449611--12449794	42	4.4	42	90	2	282	28	19	23	28	1.98
12461472--12461504	17	1.9	17	93	0	57	45	0	12	42	1.41
12462826--12463174	126	2.8	124	89	2	529	30	16	22	31	1.95
12462844--12463174	124	2.6	126	89	3	517	30	16	22	31	1.95
12466319--12466714	23	15.9	23	74	21	322	28	0	24	46	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12466325--12466386	29	2.1	29	100	0	124	25	0	29	45	1.54
12466319--12466714	52	7.9	45	73	23	227	28	0	24	46	1.58
12466319--12466714	97	4.0	98	86	9	486	28	0	24	46	1.58
12466421--12466578	29	5.6	32	75	21	101	29	0	22	47	1.52
12466549--12466599	22	2.5	21	87	9	70	25	0	29	45	1.54
12466530--12466710	51	3.6	51	78	7	228	27	1	26	44	1.64
12466939--12466983	21	2.1	21	84	8	56	4	22	33	40	1.74
12467894--12467918	7	3.6	7	100	0	50	60	12	0	28	1.32
12469067--12469151	29	3.2	29	63	27	78	42	0	25	31	1.56
12469060--12469182	51	2.4	51	95	1	221	43	0	27	28	1.61
12469163--12469197	10	3.2	11	88	12	54	45	0	37	17	1.48
12469728--12469761	2	17.0	2	100	0	68	50	0	0	50	1.00
12477238--12477285	21	2.3	20	79	10	53	47	12	4	35	1.60
12483349--12484458	44	25.2	44	63	9	247	30	19	24	24	1.98
12483302--12484487	132	9.0	132	92	0	1940	30	19	24	24	1.98
12484576--12484738	44	3.7	44	77	12	156	30	20	22	26	1.99
12484578--12484697	45	2.7	43	80	13	127	29	20	24	26	1.99
12484665--12484776	44	2.5	44	82	5	129	30	19	20	29	1.97
12485062--12485115	19	2.8	19	94	0	90	37	11	16	35	1.84
12485075--12485138	19	3.0	22	86	8	80	37	6	17	39	1.75
12485577--12485607	15	2.1	14	94	5	53	38	0	0	61	0.96
12485868--12485980	51	2.2	52	81	6	133	31	6	6	55	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12497952--12497992	19	2.2	19	95	0	73	19	17	29	34	1.94
12498892--12498943	23	2.3	22	78	15	52	17	11	3	67	1.36
12499185--12499227	21	2.0	21	100	0	86	13	23	39	23	1.90
12503944--12504274	69	4.8	69	78	5	285	40	16	21	22	1.91
12503943--12504274	138	2.4	137	77	6	339	40	16	21	21	1.91
12515260--12515298	19	2.1	19	90	0	60	71	7	2	17	1.21
12526454--12526524	27	2.6	27	80	8	81	33	16	30	18	1.93
12537126--12537260	40	3.4	40	83	9	163	38	22	19	19	1.93
12537300--12537412	41	2.8	41	91	0	190	20	21	24	33	1.97
12537984--12538015	15	2.1	15	94	0	55	25	0	34	40	1.56
12537993--12538030	14	2.7	15	84	12	53	26	2	28	42	1.69
12541668--12541705	15	2.4	17	86	8	53	28	0	2	68	1.03
12542812--12542884	27	2.7	25	75	14	65	27	5	1	65	1.22
12543073--12543366	43	6.8	43	85	2	169	25	17	29	27	1.97
12543053--12543344	86	3.4	84	78	7	266	25	17	29	27	1.97
12543114--12543366	86	2.9	85	84	2	317	25	17	30	26	1.98
12543070--12543366	129	2.3	130	82	2	375	25	17	30	27	1.97
12547534--12547743	91	2.3	91	85	2	278	40	12	13	33	1.82
12547654--12547715	29	2.1	31	93	6	110	41	17	11	29	1.84
12547942--12548028	31	2.7	31	91	7	131	33	3	0	63	1.11
12547990--12548029	20	2.0	20	85	14	55	30	5	0	65	1.14
12548223--12548346	29	4.1	29	69	11	106	41	16	12	29	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12549134--12549178	3	15.0	3	100	0	90	33	0	0	66	0.92
12549487--12549552	28	2.3	29	82	12	84	59	0	1	39	1.07
12549489--12549546	11	5.9	10	76	15	59	60	0	0	39	0.97
12549507--12549553	18	2.7	18	81	12	53	61	0	2	36	1.08
12549537--12549593	21	2.7	21	89	8	80	45	0	5	49	1.24
12549945--12549987	21	2.0	22	95	4	79	27	4	2	65	1.25
12552014--12552060	24	1.9	24	82	4	58	46	4	10	38	1.58
12552979--12553108	36	3.5	37	73	10	115	9	27	13	50	1.71
12561544--12561629	27	3.3	27	74	18	76	60	3	1	34	1.21
12562622--12562654	13	2.6	13	90	4	50	18	3	27	51	1.60
12568612--12568706	44	2.2	44	94	1	165	24	33	11	30	1.91
12583401--12583429	11	2.5	12	88	11	51	62	0	13	24	1.32
12583404--12583430	11	2.5	11	100	0	54	59	0	14	25	1.36
12583817--12583854	19	2.0	19	94	0	67	47	2	5	44	1.39
12599567--12599600	17	2.0	17	100	0	68	29	17	0	52	1.45
12601310--12601375	25	2.6	25	82	0	78	25	22	24	27	2.00
12606021--12606058	20	1.9	20	88	0	58	23	0	26	50	1.50
12606888--12606944	26	2.2	26	96	0	105	29	17	17	35	1.93
12610055--12610113	30	2.0	30	83	6	75	40	11	16	30	1.85
12610347--12610480	50	2.7	50	82	3	162	24	18	26	30	1.98
12610545--12610596	27	1.9	27	96	0	95	19	21	30	28	1.97
12610508--12610775	102	2.6	101	93	2	455	20	18	27	33	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12610651--12610742	27	2.9	32	84	13	113	17	22	27	32	1.96
12613097--12613121	8	3.1	8	100	0	50	24	0	0	76	0.80
12622292--12622334	14	3.0	14	86	3	59	44	0	2	53	1.13
12622293--12622336	5	9.2	5	85	7	56	40	0	2	56	1.11
12622297--12622343	15	3.2	14	80	14	51	38	2	4	55	1.31
12625512--12625979	237	2.0	237	92	0	785	25	21	11	40	1.88
12629888--12629931	19	2.5	17	78	10	52	59	6	15	18	1.58
12632350--12632392	20	2.2	20	86	0	59	34	4	11	48	1.60
12634534--12634591	12	4.8	12	80	2	71	51	1	32	13	1.51
12636865--12636935	32	2.2	32	85	7	90	19	12	30	36	1.89
12638669--12638807	56	2.5	57	88	6	198	25	17	6	51	1.69
12638788--12638819	6	5.3	6	100	0	64	15	15	0	68	1.21
12647072--12647219	54	2.6	54	85	10	190	25	14	13	45	1.82
12647436--12647483	18	2.5	19	86	6	62	12	6	8	72	1.26
12647681--12647717	19	2.0	19	89	5	58	27	16	0	56	1.40
12649326--12649389	32	2.0	32	100	0	128	37	6	12	43	1.68
12649938--12649984	24	2.0	24	86	0	67	46	4	4	44	1.42
12652521--12652572	23	2.3	23	86	0	68	36	1	13	48	1.54
12652553--12652608	13	4.5	13	82	13	82	33	1	16	48	1.56
12652540--12652608	36	1.9	36	93	0	120	36	1	14	47	1.53
12653261--12653398	69	2.0	69	100	0	276	31	11	31	24	1.91
12660734--12660778	13	3.7	13	82	17	69	37	0	15	46	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12660727--12660778	23	2.3	23	89	0	77	36	0	15	48	1.45
12660736--12660780	23	2.0	23	100	0	90	35	0	17	46	1.49
12662177--12662204	6	4.7	6	100	0	56	32	0	0	67	0.91
12669037--12669107	22	3.2	22	86	7	99	33	29	1	35	1.67
12669078--12669136	30	2.0	30	93	6	102	32	37	0	30	1.58
12669108--12669149	22	1.9	22	90	0	66	33	33	0	33	1.58
12669347--12669380	15	2.3	15	90	5	52	26	0	5	67	1.13
12671583--12671847	124	2.1	123	87	2	379	30	22	16	29	1.96
12674790--12674850	20	3.0	20	88	4	79	47	0	14	37	1.45
12674789--12674826	5	7.6	5	100	0	76	39	0	18	42	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