genome.fa.s3.2.7.7.80.10.50.1000.29.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  29  of  32  ( 3795 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)
5265744--5265860	16	7.3	16	72	10	87	40	0	4	54	1.26
5265761--5265867	15	6.7	15	71	13	63	41	0	2	55	1.21
5265810--5265896	30	3.0	28	70	16	77	43	1	4	50	1.30
5265937--5265968	16	2.0	16	93	0	55	53	3	0	43	1.16
5265837--5266056	112	1.9	114	81	8	263	40	4	4	50	1.43
5265815--5266089	114	2.4	112	78	7	256	40	4	5	49	1.47
5266071--5266134	17	3.9	16	77	8	67	43	1	1	53	1.19
5266130--5266186	21	2.5	22	80	11	62	40	3	3	52	1.35
5266134--5266205	37	2.0	34	84	7	90	41	2	2	52	1.30
5277643--5277674	2	16.0	2	100	0	64	0	50	0	50	1.00
5278866--5278897	2	16.0	2	100	0	64	50	0	50	0	1.00
5281563--5281616	17	3.4	16	78	17	58	61	1	1	35	1.18
5281526--5281596	29	2.3	33	76	9	78	59	2	1	36	1.21
5283493--5283521	3	9.7	3	100	0	58	31	0	0	68	0.89
5290033--5290082	19	2.5	20	75	15	59	56	0	0	44	0.99
5294039--5294066	2	14.0	2	100	0	56	0	0	50	50	1.00
5295461--5295511	6	8.3	6	77	18	52	49	0	0	50	1.00
5295457--5295511	18	3.1	17	84	10	74	45	0	0	54	0.99
5295567--5295638	36	2.0	36	100	0	144	36	25	16	22	1.94
5301533--5301568	2	18.0	2	94	0	63	52	0	47	0	1.00
5309241--5309284	23	2.0	22	82	13	54	50	0	0	50	1.00
5313255--5313331	31	2.4	32	81	12	79	48	1	0	50	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5313745--5313818	27	2.7	27	73	12	69	44	1	0	54	1.08
5317779--5321254	867	4.0	868	90	2	5020	34	15	23	27	1.95
5321397--5322324	231	4.0	231	89	1	1369	32	12	29	25	1.93
5325755--5325797	2	22.0	2	90	4	70	48	0	2	48	1.14
5326884--5326930	2	23.5	2	91	0	76	44	0	4	51	1.21
5332776--5332810	2	17.5	2	93	0	61	48	0	2	48	1.16
5345753--5345800	20	2.4	20	79	6	53	31	0	0	68	0.90
5348702--5348768	19	3.5	20	80	10	86	37	0	0	62	0.95
5353675--5353729	16	3.4	17	72	7	60	45	0	1	52	1.11
5353685--5353734	11	4.4	12	75	10	52	42	0	2	56	1.11
5354610--5354634	3	8.3	3	100	0	50	36	0	0	64	0.94
5354911--5354956	23	2.0	24	86	4	67	52	4	0	43	1.21
5358246--5358285	18	2.2	18	95	0	71	62	15	22	0	1.32
5359876--5359987	23	5.0	23	71	12	56	48	0	0	50	1.13
5359963--5360013	10	5.0	10	76	21	52	54	0	0	45	0.99
5359936--5360011	31	2.4	32	86	8	102	52	1	0	46	1.08
5359965--5360013	21	2.4	20	80	19	57	55	0	0	44	0.99
5367067--5367124	13	4.7	13	73	18	52	56	0	0	43	0.99
5367095--5367127	7	4.7	7	88	11	50	60	0	0	39	0.97
5367086--5367139	20	2.7	22	78	16	64	61	0	0	38	0.96
5367816--5367854	15	2.7	15	92	4	62	48	0	0	51	1.00
5367843--5367914	24	3.1	23	76	11	67	56	0	4	38	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5367967--5367997	4	7.8	4	100	0	62	74	0	0	25	0.82
5368710--5368749	20	1.9	21	85	10	55	12	0	30	57	1.36
5376807--5376848	18	2.3	18	87	0	57	52	2	2	42	1.27
5377094--5377118	2	12.5	2	100	0	50	52	0	48	0	1.00
5377292--5377342	22	2.3	22	86	0	66	35	5	0	58	1.22
5377286--5377339	22	2.5	22	79	14	58	35	5	0	59	1.21
5381640--5381673	15	2.1	16	89	10	52	47	0	0	52	1.00
5403741--5403786	18	2.5	18	83	16	67	65	0	2	32	1.05
5407496--5407567	24	3.0	24	78	13	69	43	4	0	52	1.20
5407596--5407673	31	2.5	32	79	8	88	48	0	1	50	1.09
5407596--5407665	32	2.2	32	84	5	88	51	0	1	47	1.09
5407652--5407699	15	3.1	15	77	17	53	52	0	0	47	1.00
5420029--5420059	15	2.1	15	100	0	62	32	12	12	41	1.81
5420545--5420609	24	2.7	24	83	7	78	40	0	0	60	0.97
5420574--5420611	18	2.1	18	90	9	60	36	0	0	63	0.95
5422428--5422482	28	2.0	28	100	0	110	29	29	7	34	1.84
5423524--5423623	46	2.2	45	84	10	132	58	5	0	37	1.20
5430198--5430239	18	2.6	16	78	14	50	33	0	0	66	0.92
5433676--5433723	20	2.3	22	82	7	64	56	0	2	41	1.11
5433884--5433939	25	2.3	25	84	9	71	57	0	0	42	0.99
5433895--5433947	22	2.5	20	81	6	61	58	0	0	41	0.98
5433909--5433958	22	2.3	22	79	6	57	56	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5434359--5434384	2	13.0	2	100	0	52	50	0	0	50	1.00
5451321--5451355	3	11.7	3	93	0	61	34	2	34	28	1.72
5451805--5451832	3	9.3	3	100	0	56	67	0	0	32	0.91
5454075--5454112	3	12.7	3	100	0	76	31	0	0	68	0.90
5456584--5456662	41	1.9	41	82	10	99	45	0	0	54	0.99
5456590--5456668	18	4.4	18	70	13	56	45	0	0	54	0.99
5457351--5457419	35	2.0	35	82	5	86	43	0	1	55	1.08
5457393--5457443	19	2.7	19	77	17	61	43	0	0	56	0.99
5463188--5463221	3	11.3	3	100	0	68	35	0	0	64	0.94
5463308--5463406	16	6.1	16	79	6	74	62	0	0	37	0.95
5463342--5463379	5	7.4	5	88	5	58	78	0	0	21	0.74
5463339--5463376	11	3.5	11	89	7	60	78	0	0	21	0.74
5463339--5463379	21	2.0	21	95	0	73	78	0	0	21	0.76
5463342--5463392	10	4.7	11	83	13	54	72	0	0	27	0.85
5463366--5463419	17	3.3	16	82	10	56	55	0	0	44	0.99
5463542--5463583	16	2.5	17	84	7	59	57	0	0	42	0.99
5464234--5464258	7	3.6	7	100	0	50	60	0	24	16	1.36
5470170--5470289	40	3.0	40	70	13	113	42	1	0	55	1.09
5470275--5470316	17	2.5	17	77	11	50	42	0	0	57	0.99
5470173--5470292	39	3.1	38	70	14	109	42	1	0	55	1.09
5470271--5470349	28	2.8	28	80	3	79	49	0	0	50	1.00
5470698--5470732	8	4.4	8	89	10	54	80	0	0	20	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5472642--5472685	21	2.0	22	82	8	54	36	2	6	54	1.40
5472650--5472697	18	2.7	19	81	12	59	39	0	2	58	1.10
5476790--5476830	15	2.5	17	84	11	50	36	7	0	56	1.27
5476809--5476870	23	2.8	21	76	11	61	37	1	1	59	1.17
5477235--5477272	15	2.3	16	86	13	51	50	0	0	50	1.00
5480757--5480786	2	15.0	2	92	0	51	50	3	0	46	1.18
5484194--5484223	2	15.5	2	93	6	53	50	0	0	50	1.00
5494386--5494437	26	2.0	26	85	7	70	30	1	1	65	1.14
5495018--5495062	22	2.0	23	91	8	74	46	0	0	53	1.00
5495192--5495253	23	2.5	24	79	7	63	41	1	6	50	1.38
5496676--5496731	19	2.9	19	81	7	60	30	1	1	66	1.12
5497376--5497433	2	29.0	2	100	0	116	50	0	0	50	1.00
5498018--5498046	5	5.8	5	100	0	58	37	0	0	62	0.96
5498581--5498647	31	2.2	32	86	10	95	62	0	0	37	0.95
5498681--5498715	19	1.9	19	88	11	56	5	20	0	74	1.02
5498661--5498704	23	2.0	23	82	13	56	2	20	0	77	0.88
5499814--5499843	2	15.0	2	100	0	60	50	0	0	50	1.00
5516003--5516028	3	8.7	3	100	0	52	30	0	0	69	0.89
5516465--5516518	20	2.5	21	76	8	56	53	3	0	42	1.18
5516460--5516524	25	2.6	25	72	16	62	49	3	0	47	1.17
5517094--5517188	30	3.2	29	78	10	102	53	0	5	41	1.23
5517081--5517202	30	4.1	29	75	16	101	54	0	4	40	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5521151--5521176	9	2.9	9	100	0	52	34	19	34	11	1.88
5522561--5522599	17	2.3	17	86	0	51	61	0	0	38	0.96
5522900--5522980	13	6.6	13	68	26	52	44	0	0	55	0.99
5522909--5522992	36	2.3	35	86	11	109	44	0	0	55	0.99
5522917--5522973	22	2.5	22	80	11	62	43	0	0	56	0.99
5522909--5523009	36	2.9	32	81	16	96	42	1	0	55	1.11
5523268--5523297	15	1.9	16	93	6	53	33	10	0	56	1.32
5531338--5531409	35	2.0	38	84	13	98	41	0	0	58	0.98
5534415--5534439	2	12.5	2	100	0	50	0	0	48	52	1.00
5535569--5535598	14	2.1	14	100	0	60	46	13	20	20	1.83

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