genome.fa.s3.2.7.7.80.10.50.1000.107.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  107  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)
33267231--33267306	8	10.2	8	83	11	65	60	0	1	38	1.05
33267231--33267357	56	2.3	53	81	12	130	61	1	3	33	1.24
33269543--33269572	13	2.3	13	94	0	51	30	6	6	56	1.51
33272369--33272456	26	3.4	25	76	6	95	46	1	3	48	1.26
33273057--33273108	10	5.7	9	80	10	52	59	1	1	36	1.19
33273054--33273113	19	3.2	19	72	11	52	53	1	1	43	1.20
33273821--33273903	40	2.1	40	97	0	157	55	7	0	37	1.28
33274302--33274349	18	2.4	21	80	10	57	29	0	4	66	1.10
33275145--33275186	16	2.6	16	85	11	50	30	0	4	64	1.14
33277864--33277898	18	2.0	17	88	5	52	14	5	2	77	1.07
33281617--33281702	43	2.0	43	93	0	145	23	24	2	50	1.61
33282900--33282940	21	1.9	22	95	5	75	58	4	2	34	1.32
33283413--33283528	29	4.0	29	76	6	110	42	19	23	14	1.88
33285242--33285309	30	2.3	32	78	17	83	30	26	1	41	1.65
33285747--33285796	26	2.0	24	84	7	64	56	0	0	44	0.99
33285751--33285789	16	2.4	16	86	0	51	56	0	0	43	0.99
33288215--33288261	24	2.0	24	91	0	76	31	19	14	34	1.92
33293748--33293782	14	2.6	14	95	4	63	62	0	0	37	0.95
33303817--33303868	25	2.1	25	96	0	95	30	19	19	30	1.96
33308116--33308188	25	3.0	23	83	13	85	36	19	12	31	1.88
33308204--33308395	24	8.3	22	69	21	99	45	21	7	24	1.78
33308314--33308508	23	8.6	23	72	8	105	47	20	9	23	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33308145--33308514	69	5.3	69	91	0	542	45	20	9	24	1.81
33308546--33308588	22	2.0	22	95	0	77	9	20	27	41	1.83
33308690--33308900	43	5.0	42	81	9	148	22	19	27	30	1.98
33308755--33308957	43	4.8	41	80	7	163	22	23	24	30	1.99
33309312--33309383	21	3.4	21	82	0	90	8	43	13	34	1.75
33320214--33320495	41	6.9	40	75	8	208	34	24	24	16	1.95
33320315--33320493	83	2.2	82	84	3	243	36	25	22	14	1.93
33320214--33320493	82	3.4	81	78	3	283	35	24	24	16	1.95
33320551--33320649	40	2.5	40	80	6	112	20	28	22	29	1.98
33320721--33320806	23	3.7	23	72	4	75	44	20	10	24	1.83
33321615--33321766	41	3.7	41	85	1	207	33	25	20	21	1.97
33329429--33329499	29	2.4	29	85	0	97	35	25	9	29	1.88
33337148--33337198	2	27.0	2	88	11	81	49	0	0	50	1.00
33340481--33340616	70	1.9	70	100	0	272	58	8	13	19	1.62
33344536--33344569	2	17.0	2	100	0	68	50	0	0	50	1.00
33350007--33350803	402	2.0	402	92	2	1339	39	15	19	25	1.91
33351229--33351258	15	1.9	16	93	6	53	10	40	0	50	1.36
33354752--33354781	1	30.0	1	100	0	60	100	0	0	0	0.00
33373174--33373227	27	2.1	26	89	6	83	48	24	20	7	1.75
33380551--33380580	16	1.9	15	93	6	51	53	3	13	30	1.56
33385023--33385295	138	2.0	138	84	2	361	21	20	24	33	1.97
33386079--33386154	20	3.8	20	89	0	116	51	0	27	21	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33386083--33386170	40	2.2	40	83	0	104	53	0	25	21	1.46
33389067--33389101	16	2.2	16	90	10	54	74	2	5	17	1.14
33389135--33389274	68	2.1	68	89	1	210	28	15	23	32	1.95
33392090--33392142	7	7.6	7	78	16	56	33	13	0	52	1.40
33393488--33393528	15	2.6	16	82	14	50	51	2	0	46	1.14
33400641--33400718	40	2.0	40	94	0	138	37	16	20	25	1.93
33412675--33412733	17	3.5	17	72	22	54	76	6	16	0	1.00
33414618--33414645	2	14.0	2	100	0	56	50	0	0	50	1.00
33418824--33418854	10	3.1	10	90	0	53	0	0	12	87	0.55
33420878--33421180	156	1.9	156	87	0	446	34	13	21	30	1.92
33424190--33424356	59	2.8	59	92	1	273	51	8	5	33	1.58
33426651--33426766	40	2.9	40	80	0	142	22	30	25	21	1.99
33431100--33431236	60	2.3	60	92	0	220	23	16	33	26	1.96
33438522--33438570	21	2.3	20	76	13	53	48	6	6	38	1.53
33446414--33446469	30	1.9	30	85	10	80	58	3	1	35	1.26
33446619--33446684	18	3.6	18	78	10	62	31	3	3	62	1.26
33447025--33447061	6	6.5	6	87	12	60	83	0	0	16	0.64
33447027--33447064	10	3.6	10	92	7	58	81	0	0	18	0.69
33447242--33447285	20	2.2	20	96	4	81	34	0	0	65	0.93
33447250--33447294	20	2.3	20	88	3	65	33	0	0	66	0.92
33447249--33447311	20	3.0	20	80	15	58	38	0	1	60	1.07
33448874--33449002	61	2.1	61	98	0	249	39	5	17	37	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33452289--33452334	15	2.9	16	87	12	60	26	0	2	71	0.97
33452487--33452566	28	2.8	27	77	12	72	30	0	5	65	1.14
33455743--33455782	20	2.0	20	100	0	80	25	30	10	35	1.88
33462039--33462088	26	1.9	26	100	0	100	30	20	16	34	1.94
33463095--33463150	21	2.7	21	75	10	60	53	3	5	37	1.41
33463738--33463912	69	2.5	68	82	5	192	44	26	6	23	1.77
33469365--33469474	25	4.5	25	70	17	70	35	22	23	18	1.96
33469418--33469483	25	2.6	26	78	9	73	37	24	19	18	1.93
33469928--33469961	5	6.6	5	93	6	59	38	20	0	41	1.53
33470484--33470543	31	2.0	30	83	9	77	23	15	0	61	1.33
33472008--33472094	23	3.7	23	83	4	104	37	16	13	32	1.88
33478099--33478148	25	2.0	25	84	0	64	28	18	24	30	1.97
33479626--33479678	26	2.0	26	96	0	97	33	18	5	41	1.74
33480219--33480264	21	2.2	21	84	0	56	23	28	4	43	1.73
33484276--33484314	20	2.0	20	89	0	60	46	10	12	30	1.75
33485648--33485698	21	2.5	20	81	6	57	35	0	21	43	1.53
33486299--33486368	25	2.8	25	74	20	65	25	24	17	32	1.96
33488748--33488782	18	2.0	18	88	5	54	37	2	2	57	1.29
33489877--33489952	28	2.7	27	83	4	71	48	14	15	21	1.80
33491942--33491969	2	14.0	2	100	0	56	50	0	0	50	1.00
33492629--33492824	97	2.0	98	91	4	317	38	25	9	27	1.86
33493632--33493662	12	2.6	12	94	0	53	70	6	0	22	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33494825--33495480	44	15.2	42	74	14	330	26	23	22	27	1.99
33495112--33495222	40	2.8	40	95	1	195	29	23	22	24	1.99
33494895--33495439	257	2.1	257	92	1	885	26	23	21	27	1.99
33494873--33495494	217	2.9	211	84	6	664	26	23	21	27	1.99
33507696--33507726	12	2.6	12	94	0	53	70	6	0	22	1.09
33508455--33508483	15	1.9	15	100	0	58	13	3	20	62	1.46
33510080--33510107	3	9.3	3	100	0	56	67	0	32	0	0.91
33510183--33510216	3	11.3	3	100	0	68	0	32	0	67	0.91
33516602--33516651	3	17.0	3	81	4	57	2	30	2	66	1.14
33516733--33516772	20	2.0	20	90	0	62	30	27	17	25	1.97
33516805--33516875	31	2.3	31	80	7	83	21	8	19	50	1.73
33518723--33518751	4	7.2	4	100	0	58	48	0	0	51	1.00
33518823--33518868	14	3.0	16	75	18	53	58	8	0	32	1.28
33518823--33518870	15	3.3	14	74	8	51	58	8	0	33	1.28
33526208--33526284	27	2.7	28	82	7	84	28	22	12	36	1.91
33526208--33526285	28	2.8	28	78	9	77	28	21	12	37	1.90
33529960--33530150	42	4.6	41	83	8	217	29	25	16	27	1.97
33532972--33533191	82	2.8	76	80	12	250	45	6	7	40	1.57
33532972--33533200	72	3.0	72	83	8	251	46	6	6	39	1.58
33533173--33533515	5	68.6	5	92	0	578	57	19	1	21	1.50
33534012--33534344	166	2.0	166	95	0	594	26	19	22	32	1.97
33544762--33544832	36	2.0	36	86	8	101	30	22	12	33	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33548453--33548524	27	2.7	26	76	4	63	20	31	16	30	1.95
33548490--33548565	27	2.8	27	87	0	107	15	35	13	35	1.87
33551303--33551465	50	3.3	50	79	13	174	43	12	12	30	1.81
33554288--33554468	46	4.0	45	78	2	182	24	22	12	39	1.89
33559652--33559880	112	2.0	112	100	0	458	43	24	14	17	1.87
33564874--33564993	45	2.7	46	82	3	172	24	22	10	42	1.85
33568616--33568684	27	2.6	27	86	4	77	15	27	24	31	1.96
33568637--33568701	27	2.4	27	89	0	94	15	27	21	35	1.94
33568785--33568958	46	3.8	46	81	2	217	25	22	9	41	1.85
33568787--33568955	91	1.8	92	88	1	259	26	21	10	42	1.84

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