genome.fa.s4.2.7.7.80.10.50.1000.15.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  15  of  31  ( 3628 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)
3613201--3613244	2	22.0	2	95	0	79	47	0	2	50	1.13
3621938--3621983	25	2.0	24	83	12	60	69	0	0	30	0.89
3621972--3622032	15	3.7	17	75	22	67	54	0	0	45	1.00
3622600--3622630	12	2.7	12	95	5	55	0	6	0	93	0.35
3622598--3622631	16	2.1	16	94	0	59	0	11	0	88	0.52
3623354--3623409	14	3.5	15	74	25	53	53	0	0	46	1.00
3624557--3624587	15	2.1	15	93	0	53	90	0	9	0	0.46
3626899--3626944	23	2.2	20	88	11	65	60	0	2	36	1.09
3627043--3627087	21	2.1	22	83	4	56	48	2	0	48	1.13
3627812--3627836	1	25.0	1	100	0	50	0	0	0	100	0.00
3629293--3629407	30	3.8	30	82	6	126	46	5	0	47	1.24
3632144--3632186	2	21.5	2	100	0	86	51	0	48	0	1.00
3645563--3645588	13	2.0	13	100	0	52	0	7	0	92	0.39
3645560--3645588	14	2.0	15	93	6	51	0	10	0	89	0.48
3647799--3647839	13	3.4	12	78	21	50	70	0	0	29	0.87
3647903--3647965	30	2.1	30	91	5	101	34	0	1	63	1.04
3647961--3648123	30	5.3	30	77	9	143	53	1	3	41	1.27
3653848--3653874	2	13.5	2	100	0	54	51	0	0	48	1.00
3653874--3653899	2	13.0	2	100	0	52	50	0	50	0	1.00
3655211--3655289	39	2.0	39	97	0	149	36	5	7	50	1.53
3655374--3655415	18	2.4	17	84	7	57	30	0	0	69	0.89
3655726--3655751	2	13.0	2	100	0	52	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)
3661321--3661357	18	2.1	18	89	0	56	35	5	5	54	1.47
3662810--3662859	16	3.1	16	82	8	66	58	0	0	42	0.98
3663746--3663787	2	21.0	2	100	0	84	50	0	0	50	1.00
3664199--3664246	13	3.4	14	78	16	53	35	0	2	62	1.07
3664424--3664472	21	2.2	21	82	7	53	34	6	0	59	1.22
3664484--3664527	21	2.0	22	86	4	63	59	0	0	40	0.98
3666434--3666467	3	11.3	3	100	0	68	35	0	0	64	0.94
3666610--3666647	17	2.2	18	85	4	51	50	0	0	50	1.00
3667522--3667564	21	2.0	21	86	0	59	32	4	2	60	1.30
3668012--3668045	7	4.9	7	85	0	50	58	0	0	41	0.98
3674162--3674198	2	18.5	2	100	0	74	51	0	0	48	1.00
3674581--3674645	18	3.8	17	78	9	62	47	0	3	49	1.17
3674939--3674985	16	2.8	16	87	6	58	65	0	0	34	0.93
3682244--3682309	21	3.0	22	80	8	73	45	0	0	54	0.99
3685297--3685338	19	2.3	19	80	8	52	52	0	4	42	1.22
3685449--3685502	21	2.5	21	78	3	54	37	5	0	57	1.22
3689639--3689669	3	10.3	3	100	0	62	67	0	0	32	0.91
3691226--3691320	46	2.0	46	84	10	120	47	0	1	51	1.07
3691226--3691321	49	2.0	49	83	8	124	47	0	1	51	1.07
3691286--3691324	20	2.0	20	84	0	51	53	0	0	46	1.00
3691262--3691321	29	2.1	29	78	9	70	53	0	0	46	1.00
3695286--3695312	3	9.0	3	100	0	54	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3695444--3695472	2	14.5	2	100	0	58	48	0	0	51	1.00
3695491--3695607	45	2.6	47	82	4	132	35	12	11	40	1.79
3695756--3695832	22	3.8	21	69	17	65	55	2	5	36	1.36
3695754--3695835	40	2.0	40	95	0	146	52	2	4	40	1.36
3695760--3695844	40	2.1	40	88	0	125	57	2	5	34	1.36
3697150--3697188	15	2.6	15	87	0	60	25	0	2	71	0.98
3697146--3697205	29	2.1	29	81	6	68	33	0	3	63	1.11
3697214--3697260	15	3.1	15	79	8	51	27	2	0	70	0.99
3697217--3697263	23	2.0	24	87	4	69	23	2	0	74	0.93
3697228--3697268	19	2.2	19	90	0	64	29	2	0	68	1.03
3697264--3697334	12	5.9	13	77	11	55	60	0	0	39	0.97
3697268--3697334	25	2.6	26	76	9	75	59	0	0	40	0.97
3697395--3697424	15	1.9	15	93	6	51	46	0	0	53	1.00
3699794--3699852	7	9.5	6	79	17	50	45	0	0	54	0.99
3699879--3699968	38	2.2	42	80	9	98	50	3	0	46	1.18
3701927--3701973	18	2.7	18	87	9	62	34	0	2	63	1.06
3702007--3702040	16	2.1	16	88	0	50	29	0	0	70	0.87
3705852--3705886	17	2.0	18	88	5	54	65	0	0	34	0.93
3711248--3711275	6	4.7	6	100	0	56	32	14	35	17	1.90
3713436--3713600	73	2.3	73	93	0	294	46	5	16	32	1.70
3715555--3715595	2	20.5	2	100	0	82	48	0	0	51	1.00
3717754--3717808	15	3.5	15	76	13	65	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3717761--3717812	16	3.1	18	75	13	65	40	0	0	59	0.97
3717921--3717955	2	17.5	2	93	0	61	0	48	0	51	1.00
3720873--3720901	2	15.0	2	92	7	51	51	0	0	48	1.00
3721053--3721088	16	2.2	17	90	5	56	44	0	0	55	0.99
3721063--3721142	33	2.5	33	80	11	87	46	0	1	52	1.08
3721126--3721166	13	3.2	12	86	10	55	39	0	0	60	0.96
3721117--3721183	25	2.7	25	81	9	75	40	0	1	58	1.07
3721063--3721150	34	2.6	32	79	12	86	45	0	1	53	1.07
3721141--3721215	38	2.0	38	82	10	91	38	0	4	57	1.18
3721210--3721278	27	2.6	28	86	6	99	63	1	0	34	1.03
3721243--3721286	21	2.1	21	88	12	65	68	0	0	31	0.90
3721515--3721570	18	3.1	18	76	19	62	35	0	0	64	0.94
3727312--3727390	12	7.1	12	75	12	71	45	0	0	54	0.99
3727300--3727385	31	2.9	28	76	19	93	47	0	0	52	1.00
3727321--3727372	14	3.5	14	74	23	52	51	0	0	48	1.00
3727348--3727418	18	4.3	17	73	16	60	38	0	1	60	1.06
3729798--3729830	16	2.1	16	88	11	50	57	0	0	42	0.98
3730290--3730316	6	4.5	6	100	0	54	85	0	14	0	0.61
3731633--3731733	42	2.6	37	76	19	100	41	0	6	50	1.36
3732249--3732276	5	5.6	5	100	0	56	17	0	0	82	0.68
3737681--3737715	17	2.1	17	100	0	70	28	17	17	37	1.92
3737745--3738024	144	1.9	144	96	0	515	32	20	11	36	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3740494--3740537	2	22.0	2	90	0	70	54	45	0	0	0.99
3746672--3746700	2	14.5	2	100	0	58	0	48	0	51	1.00
3750119--3750258	70	2.0	70	98	1	273	53	18	8	19	1.70
3750329--3750598	130	2.1	130	87	0	389	41	21	13	23	1.88
3755840--3755880	19	2.1	19	86	9	55	53	2	0	43	1.13
3755851--3755909	32	1.9	30	86	10	84	55	0	0	44	0.99
3755854--3755909	17	3.4	17	72	18	55	55	0	0	44	0.99
3758693--3758736	14	3.1	14	84	9	54	61	0	0	38	0.96
3767253--3767290	2	19.0	2	100	0	76	50	0	0	50	1.00
3767550--3767636	45	1.9	46	81	6	106	59	1	0	39	1.05
3767589--3767636	20	2.4	20	86	6	62	60	0	0	39	0.97
3767685--3767730	8	5.1	9	82	12	51	47	0	0	52	1.00
3770881--3771082	50	4.0	49	81	3	233	34	16	19	29	1.94
3770884--3771084	100	2.0	101	87	0	287	34	15	19	30	1.93
3775345--3775550	50	4.1	50	83	3	245	37	17	14	30	1.89
3783267--3783324	18	3.4	18	73	20	61	44	0	0	55	0.99
3783265--3783363	32	3.1	32	78	16	107	44	0	0	55	0.99
3783838--3783889	15	3.3	15	81	10	52	46	1	0	51	1.12
3783845--3783901	17	3.5	17	74	23	52	52	1	0	45	1.11
3783879--3783952	17	4.1	17	76	15	60	56	5	1	36	1.31
3784232--3784256	2	12.5	2	100	0	50	48	0	0	52	1.00
3785455--3785487	8	4.2	8	84	7	50	45	3	0	51	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3786213--3786248	2	18.5	2	88	5	56	50	0	2	47	1.15
3786520--3786592	37	2.0	37	88	0	110	63	8	4	24	1.40
3786534--3786589	17	3.1	17	73	14	58	66	5	5	23	1.34
3787886--3787923	20	2.0	20	90	10	62	31	0	5	63	1.17
3789090--3789118	2	14.5	2	100	0	58	48	0	0	51	1.00
3789678--3789707	2	15.0	2	92	0	51	53	0	0	46	1.00
3791146--3791177	4	7.8	4	93	6	55	78	0	0	21	0.76
3792936--3792996	26	2.3	26	81	10	70	34	8	1	55	1.39
3795972--3796056	38	2.2	38	81	8	102	58	2	1	37	1.18
3796164--3796193	6	5.2	6	96	4	53	46	0	0	53	1.00

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