genome.fa.s64.2.7.7.80.10.50.1000.19.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   

This is table  19  of  45  ( 5312 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)
3544802--3544860	25	2.5	24	81	10	68	47	0	0	52	1.00
3548934--3549005	27	2.5	28	80	15	85	47	6	0	45	1.29
3549341--3549373	15	2.1	15	94	5	57	51	0	0	48	1.00
3549433--3549477	21	2.2	22	84	11	60	48	6	0	44	1.29
3549664--3549825	59	2.7	59	79	6	175	60	3	4	30	1.35
3550129--3550174	19	2.6	18	89	6	67	58	0	0	41	0.98
3550350--3550390	16	2.5	17	80	7	50	53	7	0	39	1.29
3553961--3554044	36	2.3	36	92	8	136	57	3	2	36	1.29
3553982--3554034	22	2.4	22	78	12	54	58	5	1	33	1.32
3554940--3554982	17	2.6	15	80	20	50	41	2	2	53	1.26
3555599--3555662	30	2.2	31	83	16	91	40	1	0	57	1.08
3557666--3557724	28	2.1	28	93	0	100	32	13	10	44	1.77
3558788--3558835	23	2.1	23	84	7	62	43	2	8	45	1.45
3560999--3561032	2	17.0	2	100	0	68	50	0	0	50	1.00
3562244--3562329	43	2.0	42	86	11	120	59	0	3	37	1.15
3562315--3562364	24	2.1	25	85	7	68	64	0	0	36	0.94
3562315--3562364	8	6.2	8	77	13	50	64	0	0	36	0.94
3567827--3567972	11	12.2	12	69	19	65	58	0	0	40	1.08
3567875--3567928	8	6.8	8	80	16	67	48	0	1	50	1.11
3567862--3567940	32	2.4	33	85	6	108	49	0	1	49	1.09
3567859--3567930	25	2.8	26	79	14	78	51	0	1	47	1.09
3567935--3567987	7	7.4	7	83	12	72	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3567908--3567987	21	3.4	23	80	15	76	61	0	0	38	0.96
3568140--3568202	10	6.1	10	74	7	54	63	0	0	36	0.95
3568135--3568236	42	2.4	42	83	6	118	56	4	0	37	1.27
3569563--3570066	257	2.0	258	95	0	911	29	16	16	37	1.91
3571790--3571826	3	12.3	3	100	0	74	64	0	0	35	0.94
3574524--3574557	3	11.3	3	87	0	50	29	0	2	67	1.05
3577113--3577153	21	2.0	21	85	9	57	29	0	0	70	0.87
3577113--3577164	19	2.6	19	82	11	52	34	0	0	65	0.93
3578170--3578215	21	2.2	21	100	0	92	39	4	4	52	1.41
3579070--3579122	19	2.7	19	80	11	54	41	11	1	45	1.51
3579861--3579915	25	2.1	26	83	12	69	43	0	1	54	1.10
3581204--3581237	2	17.0	2	93	0	59	47	0	2	50	1.16
3581632--3581688	22	2.6	22	82	0	69	43	3	5	47	1.43
3581678--3581728	18	2.7	18	76	8	57	43	0	0	56	0.99
3581692--3581748	23	2.7	21	76	10	62	43	0	0	56	0.99
3589673--3589857	59	3.2	58	83	3	246	32	31	16	18	1.93
3589672--3589932	59	4.5	58	78	6	235	32	32	17	17	1.93
3589673--3589932	118	2.2	115	82	8	296	32	32	17	17	1.93
3589778--3589987	59	3.6	59	75	1	145	32	33	17	16	1.92
3594137--3594188	24	2.1	25	82	7	61	40	0	0	59	0.97
3594139--3594185	20	2.3	20	85	0	58	42	0	0	57	0.98
3594662--3594693	16	2.0	16	93	0	55	28	0	0	71	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3597500--3597533	16	2.1	16	88	5	50	35	0	2	61	1.11
3600558--3600591	2	17.0	2	100	0	68	0	50	0	50	1.00
3603735--3604253	113	4.6	112	76	5	424	33	18	14	33	1.91
3603891--3604097	111	1.9	111	82	2	263	34	20	14	31	1.92
3609800--3609844	21	2.1	21	87	0	63	13	17	4	64	1.44
3611416--3611479	14	4.5	14	70	14	51	46	10	3	39	1.55
3613682--3613799	25	5.1	22	71	24	75	47	0	0	51	1.06
3615387--3615412	12	2.2	12	100	0	52	7	15	0	76	0.99
3615405--3615495	29	3.1	29	76	6	87	35	9	1	53	1.41
3616146--3616195	27	1.9	26	88	8	75	26	4	22	48	1.68
3616154--3616239	28	3.2	26	79	9	93	26	8	22	43	1.81
3620865--3620917	27	2.0	27	84	0	70	13	49	3	33	1.60
3621276--3621315	20	2.0	21	85	9	57	45	0	0	55	0.99
3621865--3621911	23	2.1	22	84	11	60	57	2	2	38	1.23
3624105--3624163	31	2.0	31	86	6	86	52	0	0	47	1.00
3624868--3624920	11	5.2	11	77	13	60	62	0	0	37	0.96
3627001--3627538	50	10.8	50	86	2	722	30	20	17	31	1.95
3631899--3632236	50	6.8	50	90	2	482	30	20	17	31	1.96
3631899--3632236	150	2.3	150	91	1	534	30	20	17	31	1.96
3632643--3632687	20	2.2	20	88	0	63	60	2	0	37	1.09
3632643--3632706	21	3.1	21	77	6	60	59	3	0	37	1.13
3636849--3636884	6	6.0	6	86	0	54	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3640384--3640431	18	2.6	18	83	3	60	60	0	0	39	0.97
3640354--3640433	32	2.5	32	83	6	90	58	0	0	41	0.98
3640314--3640493	15	11.1	16	68	18	81	58	0	0	40	1.06
3640398--3640496	41	2.4	40	75	9	101	58	0	0	41	0.98
3640410--3640491	23	3.4	23	75	13	76	58	0	0	41	0.98
3640337--3640481	13	10.7	14	65	24	55	60	0	0	40	0.97
3640443--3640494	19	2.9	18	86	10	72	61	0	0	38	0.96
3640336--3640489	55	2.9	54	75	16	155	59	0	0	40	0.97
3640622--3640660	20	2.0	20	84	0	51	33	2	0	64	1.08
3640697--3640750	20	2.7	21	83	8	60	46	1	1	50	1.23
3642294--3642392	45	2.3	43	79	11	105	41	0	0	58	0.98
3643205--3643232	2	14.0	2	100	0	56	50	50	0	0	1.00
3643475--3643528	20	2.7	21	83	13	69	61	0	0	38	0.96
3644763--3644802	19	2.0	21	90	9	66	50	0	0	50	1.00
3644761--3644806	21	2.0	25	84	16	64	50	0	0	50	1.00
3645538--3645574	18	2.1	18	94	0	65	0	2	5	91	0.48
3645687--3645747	25	2.3	28	83	11	83	39	1	3	55	1.26
3646450--3646487	2	19.0	2	100	0	76	50	0	0	50	1.00
3646854--3646897	21	2.1	21	87	4	63	36	0	4	59	1.18
3648287--3648329	23	2.0	23	81	9	54	48	0	6	44	1.29
3651140--3651176	3	12.3	3	100	0	74	35	0	0	64	0.94
3664542--3664571	12	2.5	12	88	0	51	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3667677--3667727	9	5.3	10	77	15	54	39	0	1	58	1.09
3667939--3667998	11	5.9	11	74	18	58	31	1	0	66	1.01
3667937--3667996	28	2.1	29	79	14	72	31	1	0	66	1.01
3667936--3667998	20	3.2	19	74	14	65	31	1	0	66	1.01
3667946--3668000	28	1.9	29	92	3	94	32	0	0	67	0.91
3667993--3668021	13	2.1	14	93	6	51	41	0	0	58	0.98
3667937--3668022	39	2.2	39	79	10	95	36	1	0	62	1.03
3668019--3668060	21	2.0	22	85	4	59	50	0	0	50	1.00
3668504--3668551	19	2.5	19	74	12	53	47	2	2	47	1.25
3674072--3674112	10	3.9	10	87	9	55	29	2	0	68	1.03
3674072--3674135	21	3.2	20	76	10	69	29	3	0	67	1.06
3674639--3674686	19	2.5	19	74	12	53	47	2	2	47	1.25
3684353--3684378	13	2.0	13	100	0	52	30	0	0	69	0.89
3685123--3685153	2	15.5	2	100	0	62	48	0	0	51	1.00
3688118--3688144	12	2.2	12	100	0	54	51	7	0	40	1.30
3691321--3691354	17	2.0	17	100	0	68	52	23	11	11	1.70
3693043--3693071	15	2.0	15	93	6	51	75	0	24	0	0.80
3696791--3696820	15	2.1	14	93	6	51	50	0	0	50	1.00
3697880--3697919	13	2.8	15	78	21	50	42	0	0	57	0.98
3697887--3697921	13	2.8	13	91	4	54	42	0	0	57	0.99
3697966--3698024	27	2.2	27	82	8	68	47	0	0	52	1.00
3708747--3708775	2	14.5	2	100	0	58	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3713133--3713161	4	7.2	4	100	0	58	75	0	0	24	0.80
3715167--3715191	12	2.1	12	100	0	50	24	0	0	76	0.80
3716663--3716699	13	2.7	15	80	20	53	43	0	5	51	1.24
3717198--3717229	2	16.0	2	93	0	55	46	0	3	50	1.17
3717772--3717855	16	5.2	16	71	16	75	46	0	1	52	1.08
3717783--3717833	20	2.4	23	81	15	65	47	0	0	52	1.00
3722425--3722477	16	3.3	16	100	0	106	45	16	5	32	1.71
3726035--3726075	2	20.5	2	100	0	82	51	0	0	48	1.00
3726524--3726606	41	2.0	41	93	2	141	43	14	19	22	1.87
3726702--3726748	3	15.7	3	100	0	94	68	0	31	0	0.90

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