genome.fa.s6.2.7.7.80.10.50.1000.11.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: Chr1
Parameters: 2 7 7 80 10 50 1000
Length:  35726063

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   

This is table  11  of  109  ( 13028 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)
3563447--3563528	34	2.4	34	91	0	137	48	4	23	23	1.70
3573001--3573025	7	3.6	7	100	0	50	64	0	12	24	1.27
3582528--3582552	7	3.6	7	100	0	50	64	0	12	24	1.27
3585677--3585851	45	3.9	45	82	3	212	33	24	15	27	1.95
3585677--3585841	90	1.9	88	88	5	251	32	24	15	27	1.96
3589082--3589120	14	2.7	14	84	4	51	58	2	2	35	1.25
3590260--3590292	12	2.5	14	85	14	52	0	18	0	81	0.68
3594832--3594902	29	2.5	28	77	11	74	56	4	5	33	1.42
3596493--3596558	27	2.4	27	84	0	87	42	10	4	42	1.60
3612944--3612987	19	2.2	20	80	4	54	20	4	11	63	1.44
3616169--3616215	24	1.9	25	86	4	69	40	4	4	51	1.41
3617602--3617863	125	2.1	126	97	1	490	54	5	4	35	1.42
3617879--3617903	7	3.6	7	100	0	50	76	0	0	24	0.80
3619636--3619683	15	3.3	15	76	5	53	29	2	2	66	1.14
3625402--3625624	110	2.0	111	99	0	439	34	25	13	26	1.94
3644830--3644854	13	1.9	13	100	0	50	56	0	0	44	0.99
3646318--3646346	15	1.9	15	100	0	58	79	0	0	20	0.74
3649358--3649394	18	2.1	18	90	5	58	32	0	0	67	0.91
3649349--3649394	17	2.5	19	82	13	60	30	2	0	67	1.03
3653972--3654200	50	4.5	50	80	7	214	24	23	19	31	1.98
3656533--3656565	17	2.0	17	88	5	50	30	0	0	69	0.88
3696758--3696788	15	2.0	16	93	6	55	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3696795--3696843	21	2.3	22	80	13	57	28	0	2	69	1.00
3704108--3704223	47	2.5	46	77	5	133	37	18	12	30	1.89
3705180--3705212	2	16.5	2	93	0	57	54	0	0	45	0.99
3723953--3723995	21	2.0	23	86	9	63	39	6	4	48	1.51
3728748--3728879	21	6.3	21	79	8	128	12	21	18	46	1.82
3733051--3733094	22	2.0	22	82	8	54	31	0	4	63	1.14
3733877--3733932	29	1.9	29	89	7	87	23	17	19	39	1.92
3737237--3737291	25	2.2	25	93	3	92	40	16	16	27	1.89
3737244--3737293	25	2.0	25	100	0	100	36	16	20	28	1.93
3745485--3745592	15	7.2	15	63	12	60	46	7	20	25	1.77
3745481--3745598	30	3.9	30	90	5	184	48	6	20	24	1.74
3745481--3745601	60	2.0	60	95	3	217	47	6	20	25	1.74
3751792--3751865	26	3.0	26	78	9	66	51	1	9	37	1.43
3751829--3751903	24	3.2	22	78	12	78	57	2	5	34	1.35
3755159--3755200	19	2.2	19	87	8	59	59	0	2	38	1.10
3756124--3756163	21	1.9	21	85	10	55	52	0	2	45	1.14
3768888--3768952	20	3.2	20	80	10	87	60	0	3	36	1.13
3768887--3768954	21	3.3	21	80	12	95	60	0	2	36	1.12
3768896--3768963	11	6.4	11	75	17	72	57	0	2	39	1.14
3768908--3768974	31	2.2	30	92	5	116	59	0	1	38	1.06
3772219--3772274	21	2.5	22	88	8	87	57	0	3	39	1.16
3772246--3772374	40	3.5	40	77	21	170	63	0	3	33	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3772233--3772374	72	2.1	65	86	13	193	62	0	3	33	1.12
3772233--3772320	21	4.3	21	66	21	69	62	0	3	34	1.12
3772284--3772331	21	2.3	21	74	0	51	70	0	2	27	0.98
3772337--3772369	16	2.0	17	88	5	50	63	0	0	36	0.95
3773789--3773868	29	2.7	29	84	9	81	32	7	13	46	1.72
3773810--3773868	29	2.0	30	90	3	93	30	6	15	47	1.71
3773814--3773877	29	2.2	29	83	8	76	32	9	12	45	1.74
3774712--3774750	20	2.0	20	84	0	51	53	7	2	35	1.43
3774794--3774853	12	5.2	12	82	8	70	66	5	3	25	1.27
3777943--3777981	21	1.9	21	89	5	62	33	20	2	43	1.65
3786629--3786699	18	3.9	18	68	23	51	46	4	2	46	1.37
3788262--3788538	138	2.0	139	97	1	520	33	19	15	32	1.93
3790756--3790799	19	2.4	17	82	14	52	34	6	2	56	1.38
3792986--3793020	8	4.1	8	92	7	52	71	0	2	25	1.00
3798388--3798499	33	3.3	33	77	8	84	33	16	23	26	1.96
3798421--3798499	33	2.4	32	79	6	86	34	18	21	25	1.96
3807435--3807483	24	2.0	24	84	7	64	32	20	16	30	1.94
3810484--3810558	30	2.5	30	84	2	87	48	8	9	34	1.65
3814597--3814626	6	5.2	6	92	8	53	50	0	0	50	1.00
3816278--3816302	5	5.0	5	100	0	50	40	0	0	60	0.97
3816698--3816824	19	6.6	19	72	18	68	34	2	5	57	1.35
3816766--3816815	20	2.6	20	79	17	61	36	0	4	60	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3816694--3816851	9	16.7	9	66	18	54	34	3	5	57	1.36
3828633--3828680	21	2.3	21	96	0	87	20	8	16	54	1.68
3831519--3831704	41	4.5	41	91	0	291	24	25	19	30	1.98
3831519--3831758	82	2.9	82	81	8	283	25	24	18	30	1.98
3837951--3837975	5	5.0	5	100	0	50	40	0	0	60	0.97
3837947--3837995	15	3.1	16	82	11	57	36	2	2	59	1.21
3857994--3858065	28	2.6	27	78	8	83	31	20	25	22	1.98
3857994--3858105	29	4.0	29	75	6	88	29	16	25	27	1.97
3869291--3869359	35	2.0	35	86	8	97	62	1	1	34	1.13
3875741--3875785	18	2.5	19	79	17	51	62	2	0	35	1.08
3878263--3878302	17	2.4	17	91	0	62	62	2	15	20	1.43
3880643--3880672	2	15.0	2	100	0	60	50	0	0	50	1.00
3888552--3888577	12	2.2	12	100	0	52	38	0	34	26	1.57
3891122--3891168	25	1.9	25	83	12	62	53	10	4	31	1.55
3891190--3891216	11	2.5	11	100	0	54	59	14	0	25	1.36
3904478--3904525	19	2.5	19	83	6	53	29	0	8	62	1.24
3908522--3908551	2	15.0	2	92	0	51	46	0	0	53	1.00
3913121--3913148	6	4.7	6	100	0	56	50	0	35	14	1.43
3920331--3920521	102	1.9	99	80	8	219	32	18	23	25	1.97
3933041--3933108	33	2.1	32	91	2	109	27	13	25	33	1.93
3934738--3934766	6	4.8	6	100	0	58	0	17	65	17	1.27
3936432--3936481	25	2.0	25	88	0	73	4	34	4	58	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3940141--3940190	21	2.4	21	93	0	82	32	32	8	28	1.86
3940483--3940547	30	2.2	30	94	0	112	21	1	18	58	1.47
3940401--3940661	115	2.3	115	98	0	504	23	4	16	54	1.61
3951217--3951302	41	2.1	41	95	0	154	52	4	12	30	1.60
3955921--3955951	13	2.4	13	94	0	53	80	0	3	16	0.83
3957251--3957570	103	3.1	102	88	1	433	19	18	28	33	1.96
3961186--3961447	103	2.5	103	91	1	418	32	27	19	20	1.97
3970305--3970608	103	3.0	103	92	2	479	31	27	20	19	1.97
3970511--3970562	27	1.9	27	100	0	104	26	32	25	15	1.95
3988816--3988850	14	2.5	15	90	9	56	65	0	0	34	0.93
3989302--3989358	30	1.9	30	85	0	78	45	17	24	12	1.83
3990675--3990727	23	2.3	24	81	15	67	22	22	13	41	1.88
3996157--3996205	25	2.0	25	84	8	64	40	0	14	44	1.45
3996601--3996686	43	2.0	43	88	0	127	52	2	24	20	1.58
3997962--3998058	49	2.0	49	89	4	151	44	6	24	24	1.77
3998394--3998494	28	3.6	27	77	6	94	51	24	0	23	1.48
4002816--4003039	76	2.9	77	76	9	222	35	3	10	50	1.54
4003014--4003065	3	17.3	3	100	0	104	32	0	0	67	0.91
4006055--4006192	40	3.4	40	98	1	267	41	5	11	42	1.63
4008298--4008719	160	2.7	159	90	3	649	27	10	7	54	1.61
4008699--4008737	18	2.0	20	85	9	55	10	2	5	82	0.93
4008719--4008752	16	2.2	16	94	5	61	14	5	5	73	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4008853--4008905	27	2.0	27	85	3	72	58	7	3	30	1.43
4008979--4009075	43	2.3	43	76	3	97	1	34	2	62	1.13
4009075--4009113	20	2.0	20	89	0	60	5	30	0	64	1.15
4009083--4009138	15	3.7	15	76	9	69	3	30	0	66	1.09
4009100--4009155	10	5.5	10	77	10	51	1	26	0	71	0.96
4009081--4009163	30	2.7	30	92	1	130	2	28	0	68	1.02
4009107--4009176	24	3.1	23	76	14	65	1	28	0	70	0.96
4009149--4009177	13	2.2	13	100	0	58	0	37	0	62	0.96
4009057--4009172	20	5.8	20	71	18	57	2	30	0	67	1.04
4020739--4020858	34	3.5	34	94	0	204	39	14	8	38	1.76

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