genome.fa.s1.2.7.7.80.10.50.1000.23.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  23  of  52  ( 6211 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)
3549914--3549982	33	2.1	33	84	15	90	30	14	18	36	1.91
3551194--3551259	19	3.8	18	77	22	79	36	12	15	36	1.84
3551192--3551256	32	2.0	32	96	0	121	36	12	15	35	1.85
3551213--3551237	13	1.9	13	100	0	50	36	16	16	32	1.90
3551299--3551324	13	2.0	13	100	0	52	30	15	15	38	1.88
3551279--3551345	33	2.0	33	88	0	98	25	14	16	43	1.86
3553677--3553807	51	2.5	53	80	8	160	31	25	9	33	1.88
3553822--3553994	51	3.3	53	78	11	176	30	24	13	31	1.93
3553680--3554069	187	2.1	185	90	4	608	30	25	12	32	1.92
3554063--3554134	28	2.6	28	86	0	90	20	34	20	23	1.96
3553922--3554102	80	2.2	82	85	3	258	29	27	14	28	1.95
3553978--3554216	107	2.2	108	84	2	293	25	29	16	28	1.97
3554089--3554243	79	2.0	80	83	6	199	27	29	14	29	1.95
3558211--3558236	13	2.0	13	100	0	52	30	15	15	38	1.88
3558977--3559067	45	2.0	46	93	2	157	39	15	6	38	1.73
3560829--3560866	13	2.9	13	96	0	67	31	15	18	34	1.92
3562942--3562972	15	2.1	15	93	0	53	12	22	16	48	1.80
3567031--3567056	13	2.0	13	100	0	52	30	15	15	38	1.88
3569566--3569592	13	2.1	13	100	0	54	40	14	14	29	1.86
3569547--3569612	33	2.0	33	90	0	105	39	12	16	31	1.85
3570469--3570894	49	8.7	49	76	8	305	32	17	25	25	1.97
3570565--3570741	88	2.0	88	89	0	273	27	19	27	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3570654--3570899	52	4.8	52	81	6	290	32	17	25	24	1.96
3570654--3570899	101	2.4	101	89	2	368	32	17	25	24	1.96
3570944--3571238	29	10.4	27	81	9	297	18	18	30	32	1.95
3570916--3571243	57	5.8	57	81	6	337	20	17	30	31	1.96
3572724--3573000	51	5.3	51	74	13	260	31	14	27	27	1.95
3572826--3572898	28	2.6	28	91	0	110	24	19	32	23	1.97
3572695--3573067	158	2.4	154	91	3	575	31	14	27	26	1.95
3572985--3573054	25	2.6	28	86	8	92	28	20	28	22	1.98
3572987--3573054	29	2.6	25	86	9	82	29	20	26	23	1.99
3573008--3573419	79	5.2	78	80	5	413	30	14	27	27	1.95
3573074--3573418	155	2.2	155	82	5	410	31	13	26	28	1.94
3573355--3573534	51	3.5	51	83	2	202	34	12	25	27	1.92
3575891--3575916	13	2.0	13	100	0	52	38	15	15	30	1.88
3575968--3576093	19	6.7	19	74	16	102	34	16	13	35	1.88
3575955--3576030	32	2.4	32	93	0	125	35	15	14	34	1.88
3575987--3576011	13	1.9	13	100	0	50	32	16	16	36	1.90
3575999--3576091	21	4.7	20	78	7	100	31	17	13	37	1.89
3575999--3576092	40	2.3	40	98	0	179	31	17	13	37	1.89
3577785--3577841	13	3.9	13	76	24	60	35	14	17	33	1.90
3577765--3577862	32	3.0	32	96	1	178	34	12	17	35	1.87
3577763--3577860	19	5.8	18	71	28	90	33	12	17	36	1.87
3577903--3577927	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3600298--3600418	52	2.3	52	94	0	215	28	17	19	34	1.94
3600298--3600438	52	2.7	51	87	4	203	30	17	19	33	1.94
3600492--3600591	33	3.0	33	94	0	164	38	16	12	34	1.85
3600514--3600571	13	3.9	13	73	26	53	32	17	13	36	1.89
3600527--3600592	20	3.7	20	73	26	83	34	18	12	34	1.88
3601511--3602783	49	26.6	49	86	6	1711	32	17	26	24	1.97
3602829--3603041	27	7.2	27	70	18	138	31	13	34	20	1.92
3602854--3603220	37	11.1	34	75	17	278	33	12	34	19	1.89
3602833--3603182	70	5.4	62	83	10	284	32	12	34	20	1.90
3602977--3603215	37	6.9	36	85	10	320	32	12	35	19	1.89
3602983--3603215	70	3.4	70	91	5	352	31	12	36	20	1.90
3602977--3603246	104	2.6	105	87	5	399	31	12	35	20	1.90
3603192--3603339	62	2.4	63	90	3	237	26	16	32	24	1.96
3603186--3603347	32	5.2	30	86	9	200	29	15	32	22	1.95
3605256--3605281	13	2.0	13	100	0	52	30	15	15	38	1.88
3605365--3605416	20	2.6	19	79	14	52	32	15	0	51	1.43
3605388--3605426	20	1.9	20	84	5	51	28	20	0	51	1.48
3607114--3607157	19	2.2	21	88	8	65	36	4	20	38	1.73
3607733--3607757	13	1.9	13	100	0	50	36	16	16	32	1.90
3607712--3607776	33	2.0	32	88	8	96	30	15	15	38	1.88
3607746--3607798	20	2.7	20	91	2	81	28	16	18	35	1.93
3607844--3607895	13	4.5	13	73	26	62	32	13	17	36	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3607827--3607895	33	2.1	32	89	10	104	30	14	18	36	1.91
3611017--3611096	40	2.0	40	82	7	99	53	7	0	38	1.29
3611029--3611123	40	2.4	38	82	12	102	54	8	0	36	1.31
3612249--3612283	12	2.9	12	91	8	54	60	2	0	37	1.12
3613305--3613359	22	2.5	22	80	11	60	34	0	1	63	1.05
3621074--3621099	13	2.0	13	100	0	52	30	15	15	38	1.88
3621789--3621827	17	2.3	17	86	0	51	35	15	15	33	1.89
3630215--3630272	20	2.9	20	89	0	89	44	13	13	27	1.82
3638198--3638235	13	2.9	13	88	0	58	34	15	18	31	1.92
3638262--3638317	19	2.9	19	80	15	69	37	19	14	28	1.91
3638283--3638347	33	2.0	32	87	3	94	43	16	13	26	1.86
3640945--3640971	13	2.1	13	100	0	54	37	14	14	33	1.88
3645458--3645492	3	11.7	3	87	0	52	25	34	2	37	1.71
3645456--3645494	12	3.2	12	85	0	60	23	33	2	41	1.68
3649317--3649347	15	2.1	15	93	0	53	12	22	16	48	1.80
3653392--3653492	32	3.1	32	97	2	184	31	12	14	40	1.84
3653395--3653491	13	5.6	19	71	28	92	29	12	15	42	1.84
3654521--3654795	76	3.6	75	84	6	261	40	12	19	27	1.88
3654655--3654922	126	2.1	126	82	6	337	37	11	22	28	1.88
3654799--3654964	78	2.1	80	84	4	212	36	11	23	28	1.90
3656074--3656129	19	2.9	19	83	2	76	35	19	8	35	1.83
3656158--3656210	20	2.7	20	79	5	63	32	13	20	33	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3662697--3662957	68	3.9	68	76	3	213	28	12	19	38	1.89
3662697--3662957	136	1.9	135	84	2	344	28	12	19	38	1.89
3670771--3670802	16	2.0	16	93	0	55	46	0	0	53	1.00
3673531--3673587	27	2.0	30	86	10	84	66	0	1	31	1.02
3674483--3674539	21	2.9	21	72	12	59	56	0	0	43	0.99
3674501--3674531	16	1.9	16	93	0	53	58	0	0	41	0.98
3675678--3675711	10	3.2	10	84	15	50	20	11	17	50	1.77
3675680--3675705	12	2.2	12	100	0	52	15	7	15	61	1.55
3678018--3678068	20	2.5	20	100	0	102	39	13	11	35	1.82
3678058--3678087	13	2.3	13	94	0	51	36	10	20	33	1.86
3682657--3682731	31	2.4	31	93	0	123	29	17	16	37	1.91
3694998--3695056	29	1.9	30	90	10	93	32	0	33	33	1.58
3695026--3695132	54	2.0	55	92	1	180	35	0	29	34	1.58
3695817--3695881	33	2.0	33	87	3	96	29	15	13	41	1.86
3696759--3696790	15	2.1	16	94	5	57	40	0	0	59	0.97
3698629--3698677	20	2.5	20	86	0	71	38	8	20	32	1.82
3924752--3924778	13	2.1	13	100	0	54	29	14	14	40	1.86
3924762--3924820	19	3.1	19	85	2	82	37	15	13	33	1.86
3924863--3924892	13	2.3	13	94	0	51	36	16	13	33	1.88
3924848--3924912	33	2.0	33	84	6	87	33	10	18	36	1.86
3926069--3926349	141	2.0	142	95	0	510	32	11	16	39	1.85
3931897--3932169	88	3.1	88	83	5	311	34	10	22	31	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3932672--3932705	17	2.0	17	100	0	68	41	5	17	35	1.74
3934187--3934238	19	2.7	20	87	3	79	28	15	15	40	1.88
3940200--3940235	13	2.8	13	91	0	54	38	16	8	36	1.79
3942131--3942189	22	2.9	20	85	11	84	38	0	27	33	1.57
3942131--3942189	21	2.9	21	88	11	88	38	0	27	33	1.57
3942739--3942895	72	2.2	72	92	0	260	42	18	19	20	1.90
3942998--3943049	20	2.6	20	84	0	59	40	11	17	30	1.85
3944479--3944534	23	2.6	21	80	8	69	33	16	12	37	1.86
3947344--3948003	110	6.0	110	94	0	1149	27	12	21	38	1.89
3949948--3949972	7	3.6	7	100	0	50	28	40	0	32	1.57

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