genome.fa.s3.2.7.7.80.10.50.1000.14.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  14  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)
3879205--3879256	19	2.8	20	77	11	56	65	1	3	28	1.21
3879148--3879296	70	2.2	67	80	8	167	61	1	4	32	1.25
3879700--3879975	88	3.1	86	74	14	254	32	10	18	38	1.86
3881631--3881669	2	19.5	2	100	0	78	48	0	0	51	1.00
3882540--3882936	189	2.0	189	88	8	584	39	12	14	33	1.84
3888547--3888605	3	19.7	3	100	0	118	33	0	0	66	0.92
3890319--3890343	9	2.8	9	100	0	50	8	0	0	92	0.40
3906518--3906548	4	7.8	4	100	0	62	25	0	0	74	0.82
3914122--3914207	38	2.3	38	83	0	100	54	6	3	34	1.44
3915246--3915279	12	2.8	12	86	0	50	52	0	2	44	1.16
3916150--3916207	28	2.1	27	82	17	68	46	0	1	51	1.11
3916305--3916393	39	2.3	39	86	5	117	39	5	5	49	1.50
3916446--3916478	16	2.1	16	94	5	59	57	0	0	42	0.98
3929489--3929542	29	1.9	27	85	7	72	40	7	0	51	1.30
3939737--3939791	28	2.0	28	85	7	76	40	0	1	58	1.09
3939734--3939790	19	3.1	19	82	7	64	40	0	1	57	1.09
3940150--3940215	22	3.0	23	73	4	64	50	0	6	43	1.27
3945407--3945506	9	10.8	9	69	17	53	35	2	0	63	1.06
3945450--3945590	11	13.9	11	70	23	62	36	2	0	60	1.17
3945404--3945552	40	3.9	39	89	7	227	33	2	0	63	1.08
3945461--3945516	29	1.9	29	82	7	69	32	5	0	62	1.18
3945526--3945590	10	6.2	10	78	16	60	41	1	1	55	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3946230--3946292	22	2.8	22	87	4	81	49	3	1	46	1.27
3946269--3946306	16	2.4	16	90	0	58	47	5	5	42	1.48
3946351--3946534	93	2.0	93	95	0	332	39	4	6	48	1.50
3946576--3946615	22	1.9	20	85	10	53	57	5	2	35	1.34
3947209--3947233	2	12.5	2	100	0	50	48	0	0	52	1.00
3948537--3948588	20	2.7	19	77	8	52	48	1	0	50	1.12
3950120--3950152	2	16.5	2	100	0	66	51	0	0	48	1.00
3950912--3951075	26	6.5	26	68	14	85	39	18	20	21	1.92
3952255--3952389	41	3.5	40	75	11	127	32	23	16	27	1.96
3953265--3953347	4	20.5	4	71	20	50	3	21	3	71	1.17
3953277--3953331	10	5.5	10	80	6	58	3	18	5	72	1.18
3953277--3953341	29	2.2	29	91	0	103	4	18	4	72	1.20
3953302--3953363	17	3.8	16	78	17	56	6	19	3	70	1.22
3953364--3953441	5	15.6	5	75	14	56	53	1	1	43	1.16
3957743--3957899	78	2.0	78	97	0	296	33	10	14	42	1.79
3964411--3964468	29	2.0	29	83	12	75	48	5	18	27	1.70
3967667--3967840	88	2.0	88	97	0	330	39	20	14	24	1.91
3969122--3969149	14	2.0	14	100	0	56	42	14	21	21	1.88
3976387--3976475	47	2.0	43	84	8	115	43	3	3	49	1.35
3976814--3976926	4	27.5	4	71	19	65	65	0	34	0	0.93
3976821--3976970	14	10.8	14	69	19	73	64	0	36	0	0.94
3976849--3976942	33	3.0	30	71	14	91	65	0	34	0	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3976860--3976957	21	4.9	19	76	19	92	67	0	32	0	0.91
3976812--3976990	63	2.9	62	80	10	154	64	0	35	0	0.94
3977301--3977325	13	1.9	13	100	0	50	64	8	20	8	1.46
3982167--3982219	26	2.0	26	89	7	81	45	7	1	45	1.42
3982401--3982465	3	21.7	3	100	0	130	67	32	0	0	0.91
3982464--3982498	3	11.3	3	87	6	52	62	5	0	31	1.18
3982718--3982793	27	2.8	27	81	0	98	17	28	27	26	1.97
3982834--3982873	18	2.2	18	86	4	53	12	0	17	70	1.18
3986224--3986263	2	20.0	2	94	0	71	47	0	2	50	1.14
3987691--3987772	31	2.6	31	84	3	112	43	12	10	32	1.77
3989616--3989667	24	2.2	24	89	0	77	50	7	3	38	1.50
3990361--3990412	24	2.2	24	85	0	68	51	9	3	34	1.53
3995670--3996462	132	6.0	132	83	6	937	28	24	19	27	1.98
3995666--3996466	264	3.0	263	87	3	1091	28	24	19	28	1.98
3995730--3996462	397	1.8	398	88	2	1134	28	24	19	27	1.98
3996472--3997294	89	9.3	88	89	3	888	22	24	25	27	2.00
3996472--3997289	178	4.6	176	88	2	1075	22	24	25	27	2.00
3996472--3997289	354	2.3	354	86	2	1131	22	24	25	27	2.00
3996740--3997238	44	11.3	44	65	11	232	21	23	28	26	1.99
3998468--3998498	13	2.3	14	94	5	55	12	12	0	74	1.08
3998989--3999113	1	125.0	1	69	0	79	1	4	8	84	0.82
3998989--3999113	10	13.3	9	74	17	103	1	4	8	84	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3998989--3999113	14	8.9	14	73	11	103	1	4	8	84	0.82
3998988--3999114	27	4.6	27	82	10	127	1	4	10	83	0.86
4004081--4004140	3	19.7	3	74	16	52	61	3	3	31	1.28
4008670--4008822	22	7.0	22	90	0	225	26	26	14	32	1.94
4023139--4023175	18	2.1	17	90	5	56	35	5	8	51	1.55
4023299--4023357	30	2.1	26	87	12	82	49	0	0	50	1.00
4025464--4025500	2	18.5	2	100	0	74	51	0	48	0	1.00
4027648--4027687	3	13.3	3	100	0	80	32	0	0	67	0.91
4028997--4029080	41	2.0	41	95	0	150	26	11	16	45	1.82
4029140--4029197	19	2.8	22	72	17	61	1	20	0	77	0.86
4029145--4029189	18	2.5	19	85	7	58	2	17	0	80	0.82
4029153--4029186	14	2.5	13	86	9	50	2	11	0	85	0.71
4045431--4046130	114	6.2	114	89	1	1048	29	19	23	27	1.98
4049213--4049245	10	3.1	11	86	8	50	33	9	21	36	1.85
4049290--4049381	13	6.9	13	71	18	73	45	8	3	42	1.51
4049290--4049398	40	2.7	40	88	2	157	44	10	3	41	1.55
4049413--4049473	17	3.5	17	84	4	77	45	13	0	40	1.43
4049413--4049501	18	4.8	18	76	14	92	46	13	0	40	1.43
4049404--4049496	17	4.6	21	70	24	67	45	13	0	40	1.44
4049413--4049496	39	2.2	38	85	10	111	45	14	0	40	1.45
4050084--4050114	16	1.9	16	93	0	53	54	22	0	22	1.44
4050022--4050378	25	14.2	25	73	6	247	45	18	3	32	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4050022--4050415	9	47.0	9	65	15	166	45	19	3	31	1.65
4050363--4050415	25	2.1	25	85	0	70	45	26	1	26	1.64
4050138--4050379	75	3.2	75	93	2	432	44	17	3	34	1.65
4050327--4050415	41	2.2	41	83	0	106	46	22	2	29	1.64
4052227--4052257	14	2.1	15	94	5	55	29	0	32	38	1.57
4052320--4052358	17	2.4	16	84	12	53	30	0	33	35	1.58
4052327--4052359	17	1.9	17	93	0	57	27	0	36	36	1.57
4052685--4052715	12	2.5	12	94	5	53	70	0	3	25	1.02
4052700--4052752	20	2.7	20	80	11	56	67	7	1	22	1.25
4052690--4052742	19	2.9	18	81	10	63	73	3	1	20	1.08
4053044--4053321	84	3.3	81	81	6	315	25	18	24	30	1.98
4055632--4055790	9	16.8	9	68	21	51	47	10	1	39	1.49
4055641--4056118	56	8.2	56	79	12	495	45	11	2	40	1.54
4055738--4055788	22	2.4	22	86	3	77	47	9	1	41	1.48
4055831--4055906	16	4.6	16	67	23	59	44	18	1	35	1.58
4055831--4055907	9	9.2	9	72	23	62	44	18	1	36	1.58
4055641--4056118	121	4.1	109	75	15	347	45	11	2	40	1.54
4055834--4055907	25	3.0	24	75	16	80	43	18	1	36	1.59
4055831--4056033	50	4.1	50	71	17	160	45	13	1	39	1.52
4055959--4056001	22	2.0	22	81	9	52	51	11	0	37	1.39
4055893--4056062	34	5.2	34	80	13	187	45	11	1	41	1.50
4056039--4056084	22	2.1	22	91	0	74	45	10	0	43	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4055959--4056123	90	1.8	90	88	5	253	46	10	2	41	1.51
4056105--4056322	9	26.2	9	67	17	96	41	16	3	37	1.67
4056110--4056141	16	2.0	16	100	0	64	43	25	0	31	1.55
4056163--4056277	34	3.2	34	74	15	99	43	18	1	36	1.60
4056194--4056244	16	3.1	16	88	5	75	43	21	1	33	1.64
4063459--4063672	43	5.0	42	77	4	194	22	16	30	30	1.96
4063474--4063642	86	2.0	86	91	0	275	21	16	31	30	1.95
4063481--4063674	86	2.3	86	86	0	262	23	16	30	29	1.96
4063825--4063869	22	2.1	21	91	4	72	42	28	17	11	1.84
4064419--4064527	25	4.4	25	78	5	89	32	22	26	18	1.97

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