genome.fa.s3.2.7.7.80.10.50.1000.129.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  129  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)
38935841--38936211	44	8.5	41	79	13	350	28	21	23	26	1.99
38935841--38936211	89	4.2	86	77	13	359	28	21	23	26	1.99
38935836--38936174	128	2.6	129	79	13	356	28	21	23	26	1.99
38936396--38936499	19	5.4	19	87	4	145	39	10	15	34	1.82
38936397--38936499	40	2.6	40	92	3	165	39	10	14	34	1.81
38937218--38937266	25	2.0	25	95	0	89	30	8	4	57	1.47
38937940--38938136	98	2.0	98	94	0	349	28	10	23	37	1.88
38938983--38939017	9	3.7	10	88	11	56	0	8	0	91	0.42
38939310--38939355	22	2.1	22	84	15	60	43	19	6	30	1.76
38944900--38944967	35	1.9	36	96	3	129	35	8	7	48	1.62
38945177--38945219	17	2.6	16	82	10	52	55	0	2	41	1.12
38946178--38946223	18	2.5	19	86	13	62	32	30	0	36	1.58
38949908--38950100	50	3.7	50	86	4	242	25	21	29	23	1.99
38957192--38957384	50	3.8	50	85	0	242	20	29	23	26	1.99
38957192--38957384	100	1.9	101	86	1	271	20	29	23	26	1.99
38968360--38968423	28	2.3	28	78	10	69	56	0	0	43	0.99
38972868--38972941	31	2.4	31	86	0	94	51	16	9	22	1.73
38975362--38975394	17	1.9	17	93	0	57	27	6	3	63	1.32
38975367--38975402	17	2.1	17	89	5	54	27	8	5	58	1.50
38975533--38975561	13	2.1	14	93	6	51	75	0	6	17	1.01
38984881--38985144	46	5.8	46	96	0	469	32	16	21	28	1.95
38987783--38987841	12	4.8	12	76	17	50	22	0	1	76	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38987783--38987841	19	3.2	18	81	11	66	22	0	1	76	0.88
38987802--38987841	4	10.5	4	80	20	50	25	0	0	75	0.81
38987792--38987849	26	2.3	27	85	8	77	22	1	1	74	1.01
38987792--38987849	15	3.9	15	77	18	59	22	1	1	74	1.01
38987783--38987848	7	10.0	7	80	11	61	22	1	1	74	0.99
38988000--38988050	22	2.3	23	83	10	70	27	45	9	17	1.80
38988984--38989174	99	1.9	100	88	5	289	26	16	26	30	1.97
38989161--38989202	17	2.4	18	76	19	52	73	2	0	23	0.94
38989165--38989200	16	2.2	17	90	5	56	72	2	0	25	0.98
38989786--38989815	15	2.0	15	93	0	51	50	0	10	40	1.36
38995271--38995334	32	2.0	32	100	0	128	28	9	18	43	1.81
38996087--38996121	18	1.9	18	88	0	52	71	2	14	11	1.25
38996259--38996331	25	2.9	25	82	10	69	36	5	19	38	1.75
38996271--38996331	25	2.4	25	86	5	79	34	4	22	37	1.76
39003162--39003301	64	2.2	64	89	0	217	34	13	15	36	1.87
39003159--39003322	32	5.1	32	78	1	159	32	12	15	39	1.84
39004345--39004377	17	2.0	17	88	5	50	33	0	21	45	1.52
39010295--39010352	30	1.9	30	85	0	80	43	5	22	29	1.75
39010564--39010595	13	2.5	13	94	0	55	31	0	12	56	1.37
39010690--39010938	50	4.8	50	86	3	291	26	21	30	22	1.99
39010690--39010939	100	2.4	103	85	5	326	26	21	30	22	1.99
39014551--39014683	40	3.5	40	72	10	132	32	21	24	21	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39014512--39014727	75	2.9	73	83	6	263	31	22	25	19	1.98
39014509--39014654	35	4.1	34	75	9	123	33	23	25	17	1.96
39015050--39015131	35	2.3	35	93	0	137	37	14	30	17	1.89
39017849--39017911	18	3.6	18	72	10	58	52	7	3	36	1.47
39018131--39018169	15	2.5	15	88	12	53	76	0	2	20	0.90
39018262--39018298	18	2.1	18	94	0	65	70	2	5	21	1.20
39018578--39018672	47	2.0	48	91	2	156	31	27	30	10	1.90
39021135--39021184	19	2.6	20	84	12	61	36	2	6	56	1.36
39025493--39025557	23	2.7	23	75	13	69	44	3	1	50	1.26
39027382--39027409	2	14.0	2	100	0	56	50	0	0	50	1.00
39027415--39027457	15	2.8	16	79	10	54	60	2	0	37	1.10
39028208--39028242	18	1.9	18	88	0	52	74	17	8	0	1.06
39035192--39035240	17	2.9	17	84	6	64	65	0	28	6	1.16
39036292--39036334	21	2.0	21	95	0	77	27	27	20	23	1.99
39038724--39038794	22	3.2	22	93	0	115	25	28	15	30	1.96
39039816--39040009	50	3.8	51	75	5	153	25	24	20	29	1.99
39040089--39040221	58	2.3	58	84	2	169	21	25	26	27	1.99
39042831--39042879	24	2.0	25	84	4	64	32	22	24	20	1.98
39051362--39051403	16	2.8	16	78	7	52	38	21	0	40	1.53
39057054--39057166	19	5.8	19	89	4	181	38	10	15	36	1.82
39057055--39057166	40	2.8	40	95	2	201	38	10	14	36	1.81
39057054--39057173	59	2.1	56	89	6	179	38	10	15	36	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39057938--39057991	26	2.1	26	86	3	74	27	7	5	59	1.47
39058670--39058866	98	2.0	98	95	0	358	28	10	24	37	1.88
39060027--39060072	24	1.9	24	86	0	65	45	19	23	10	1.82
39063466--39064144	133	5.1	133	90	2	909	29	18	23	28	1.98
39065466--39065662	98	2.0	98	93	0	340	28	10	23	38	1.87
39066539--39066628	17	4.9	18	70	18	53	46	0	2	51	1.13
39066569--39066635	24	2.9	24	71	20	61	43	0	1	55	1.09
39071334--39071392	18	3.1	18	73	21	50	40	1	35	22	1.64
39073510--39073943	218	2.0	217	98	0	841	21	18	15	44	1.86
39078280--39078355	31	2.5	31	77	0	80	32	11	10	44	1.75
39080956--39080983	14	2.0	14	100	0	56	57	0	0	42	0.99
39089112--39089161	2	25.0	2	100	0	100	50	0	0	50	1.00
39098417--39098469	16	3.3	16	94	0	88	37	3	32	26	1.74
39098449--39098536	44	2.0	44	86	2	122	29	4	27	38	1.76
39098656--39098716	18	3.3	18	84	9	79	59	1	3	36	1.24
39102101--39102201	51	2.0	52	84	9	136	34	12	14	37	1.85
39102542--39102573	14	2.3	14	100	0	64	21	6	12	59	1.55
39102686--39103011	90	3.6	90	88	0	492	26	6	15	51	1.66
39106023--39106102	25	3.2	25	70	7	72	36	15	25	23	1.93
39106157--39106207	25	2.0	25	88	0	75	31	21	27	19	1.97
39106280--39106339	25	2.4	25	80	5	68	41	18	23	16	1.90
39106295--39106342	25	1.9	25	91	0	78	41	22	18	16	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39108626--39108680	5	10.0	5	81	18	65	20	21	0	58	1.40
39108629--39108680	11	4.6	11	81	13	61	21	23	0	55	1.43
39108626--39108679	28	1.9	28	88	7	83	18	22	0	59	1.38
39108682--39108734	21	2.7	20	81	16	58	24	9	0	66	1.21
39108682--39108729	20	2.4	21	86	6	64	27	10	0	62	1.27
39108705--39108763	16	3.6	16	82	10	75	18	11	1	67	1.30
39108659--39108791	57	2.3	57	76	12	130	23	12	1	62	1.38
39108620--39108763	17	8.2	17	74	16	80	20	15	0	63	1.34
39109004--39109046	21	2.0	21	82	8	52	32	6	0	60	1.23
39109232--39109434	27	8.0	27	69	20	129	23	11	0	64	1.29
39109265--39109461	49	4.0	49	88	4	281	22	11	1	64	1.32
39109265--39109461	98	2.0	99	91	3	317	22	11	1	64	1.32
39109349--39109471	21	5.4	21	69	21	63	23	10	0	65	1.29
39109494--39109730	44	5.4	44	90	0	339	35	2	12	48	1.55
39113539--39113686	45	3.3	44	79	14	128	37	5	3	54	1.40
39113561--39113648	23	3.9	23	78	10	92	37	3	2	56	1.28
39121063--39121115	20	2.7	20	82	2	63	50	0	1	47	1.12
39121512--39121578	31	2.1	32	91	5	109	47	7	5	38	1.56
39122113--39122172	28	2.1	28	82	11	70	55	8	6	30	1.55
39125078--39125124	16	3.1	15	79	8	60	36	0	2	61	1.08
39130219--39130249	11	2.8	11	90	0	53	67	0	0	32	0.91
39130456--39130497	20	2.0	20	86	4	57	61	4	0	33	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39130524--39130562	15	2.6	15	95	0	69	64	0	0	35	0.94
39130525--39130562	7	5.0	8	81	12	53	63	0	0	36	0.95
39132483--39132533	20	2.7	19	82	8	59	41	1	3	52	1.31
39139829--39140075	95	2.6	97	90	5	369	46	10	11	32	1.73
39145331--39145457	25	5.3	24	84	6	127	38	19	24	17	1.93
39166725--39166760	16	2.2	16	95	0	63	41	33	0	25	1.55
39167393--39167497	53	2.0	53	85	9	142	31	7	13	47	1.71
39167520--39167625	54	2.0	54	92	0	176	27	9	15	48	1.75
39167362--39167696	127	2.6	128	85	3	448	30	13	12	42	1.82
39167576--39167769	71	2.7	72	85	4	264	28	17	13	41	1.87

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