genome.fa.s4.2.7.7.80.10.50.1000.29.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: 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  29  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)
5644148--5644194	23	2.1	23	88	4	69	44	6	0	48	1.28
5644725--5644897	11	17.0	10	64	23	60	41	0	1	57	1.06
5644758--5644810	15	3.3	16	75	14	56	50	0	0	49	1.00
5644758--5644851	32	2.9	33	90	4	147	47	0	1	51	1.07
5644777--5644828	16	3.2	16	75	20	63	50	0	0	50	1.00
5644770--5644873	18	6.2	18	70	18	73	45	0	0	53	1.06
5644848--5644902	17	3.2	16	78	21	58	34	0	0	65	0.93
5644818--5644894	27	3.0	26	83	12	88	36	0	1	62	1.04
5646339--5646382	19	2.2	20	88	12	63	65	0	0	34	0.93
5660701--5660735	5	7.0	5	100	0	70	20	40	20	20	1.92
5666089--5666491	198	2.0	198	91	2	655	38	11	8	41	1.71
5666574--5666632	20	2.9	21	77	10	59	35	0	0	64	0.94
5666572--5666627	27	2.1	27	83	6	69	35	0	0	64	0.94
5666584--5666666	17	5.0	17	71	21	52	37	0	0	62	0.95
5666625--5666674	16	3.1	16	77	13	57	40	0	0	60	0.97
5666676--5666712	19	1.9	19	94	0	65	32	0	2	64	1.07
5666995--5667056	27	2.3	26	84	13	65	41	8	4	45	1.55
5667371--5667419	19	2.6	17	74	20	53	38	4	0	57	1.18
5669345--5669398	26	2.0	28	82	7	67	50	0	0	50	1.00
5675118--5675163	21	2.2	20	84	3	56	80	0	15	4	0.86
5675130--5675171	20	2.1	21	86	8	61	73	0	21	4	1.01
5675259--5675321	30	2.0	32	84	6	85	39	7	6	46	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5675668--5675695	2	14.0	2	100	0	56	50	0	0	50	1.00
5683073--5683108	2	18.0	2	100	0	72	50	0	0	50	1.00
5689506--5689667	58	2.8	58	89	0	243	16	17	23	42	1.88
5696967--5697013	2	24.5	2	81	16	55	46	2	0	51	1.13
5697211--5697281	20	3.5	20	80	0	79	35	11	11	42	1.77
5700557--5700610	26	2.0	27	85	3	74	53	0	0	46	1.00
5700666--5700716	15	3.1	17	73	26	56	37	0	0	62	0.95
5700675--5700719	18	2.5	19	85	7	58	31	0	0	68	0.89
5700652--5700729	22	3.7	22	67	22	60	38	0	0	61	0.96
5701086--5701151	25	2.7	24	80	15	80	54	3	0	42	1.15
5701088--5701179	12	7.3	12	71	19	64	53	4	0	42	1.21
5701078--5701185	12	8.6	12	67	23	53	52	3	0	42	1.25
5701879--5701903	2	12.5	2	100	0	50	52	0	0	48	1.00
5702602--5702631	14	2.1	14	93	0	51	40	0	0	60	0.97
5702746--5702808	25	2.8	23	79	13	69	39	0	1	58	1.07
5702818--5702846	11	2.6	11	100	0	58	68	0	0	31	0.89
5706443--5706492	24	2.1	24	100	0	100	20	26	16	38	1.92
5708663--5708697	2	17.5	2	93	0	61	0	45	2	51	1.16
5709269--5709350	29	2.9	29	80	10	91	48	1	1	48	1.17
5710435--5710459	2	12.5	2	100	0	50	52	0	0	48	1.00
5711197--5711238	17	2.5	17	77	14	50	42	0	0	57	0.99
5713567--5713625	2	29.5	2	100	0	118	0	49	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5715400--5715448	2	24.5	2	91	0	80	0	46	0	53	1.00
5718579--5718635	20	3.3	19	70	29	63	54	5	0	40	1.23
5719752--5719788	2	18.5	2	94	0	65	51	2	0	45	1.15
5719722--5719852	68	1.9	68	90	3	210	46	9	9	34	1.69
5724616--5724649	2	17.0	2	100	0	68	0	50	0	50	1.00
5726340--5726364	9	2.8	9	100	0	50	24	0	0	76	0.80
5726633--5726696	16	3.9	16	74	22	62	57	0	0	42	0.98
5730734--5730786	27	2.0	26	85	7	72	22	26	13	37	1.91
5730953--5730997	3	15.0	3	90	9	74	0	35	0	64	0.94
5731778--5731803	2	13.0	2	100	0	52	50	0	0	50	1.00
5731803--5731828	2	13.0	2	100	0	52	0	0	50	50	1.00
5732004--5732049	23	2.0	23	91	4	76	50	0	0	50	1.00
5732980--5733072	30	3.1	29	73	14	82	48	1	7	43	1.38
5733389--5733418	15	2.1	14	93	6	51	70	0	0	30	0.88
5733448--5733491	19	2.3	18	81	11	52	61	13	0	25	1.32
5733699--5733761	29	2.2	30	80	13	78	55	3	0	41	1.16
5733758--5733791	16	2.0	18	88	11	54	58	5	0	35	1.22
5734182--5734228	13	3.5	13	78	16	51	36	0	4	59	1.17
5734170--5734227	27	2.1	27	84	6	73	34	0	3	62	1.12
5734173--5734216	19	2.2	19	84	8	52	34	0	4	61	1.16
5734320--5734363	22	2.0	22	82	8	54	31	0	2	65	1.05
5738901--5738978	25	3.1	25	69	10	70	46	0	0	53	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5742568--5742605	2	19.0	2	100	0	76	50	50	0	0	1.00
5744280--5744365	43	2.0	43	83	16	110	38	0	0	61	0.96
5744284--5744365	21	3.9	20	73	22	62	39	0	0	60	0.96
5745089--5745140	22	2.4	21	81	9	61	44	1	1	51	1.23
5745246--5745280	2	17.5	2	100	0	70	51	0	0	48	1.00
5746684--5746713	15	2.0	15	93	0	51	53	3	0	43	1.17
5748303--5748344	16	2.5	18	77	18	54	54	4	4	35	1.42
5751044--5751072	9	3.3	9	95	4	51	0	0	93	6	0.36
5762526--5762551	12	2.2	12	100	0	52	26	15	7	50	1.71
5764930--5764998	33	2.1	33	91	0	111	36	23	17	23	1.95
5767294--5767321	11	2.5	11	100	0	56	32	0	0	67	0.91
5767682--5767783	52	2.0	51	90	5	161	50	0	1	47	1.19
5767848--5767885	19	2.0	19	94	0	67	52	2	5	39	1.38
5768097--5768123	2	13.5	2	100	0	54	48	0	0	51	1.00
5768360--5768411	26	2.0	26	96	0	95	25	11	32	30	1.91
5769607--5769634	2	14.0	2	100	0	56	50	0	0	50	1.00
5772143--5772175	8	4.1	8	100	0	66	63	24	12	0	1.28
5772933--5772974	16	2.8	16	80	20	54	47	0	0	52	1.00
5772962--5773000	11	3.1	14	75	24	50	58	0	0	41	0.98
5773008--5773050	16	2.6	16	85	3	59	51	4	2	41	1.35
5773075--5773124	22	2.3	22	86	3	75	56	4	0	40	1.18
5773117--5773170	14	3.6	15	82	7	65	59	5	3	31	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5773094--5773179	14	5.7	14	77	11	64	55	4	2	37	1.33
5775594--5775628	10	3.7	10	88	11	56	80	0	0	20	0.72
5775689--5775761	30	2.4	29	80	6	83	46	6	0	46	1.29
5776251--5776294	21	2.1	21	83	8	54	38	2	18	40	1.63
5780008--5780041	13	2.5	14	95	4	61	29	11	23	35	1.90
5780088--5780148	21	2.8	20	72	20	52	42	1	6	49	1.38
5782433--5782466	2	17.0	2	100	0	68	50	0	0	50	1.00
5782785--5782815	15	2.0	16	93	6	55	58	0	3	38	1.15
5783195--5783236	22	1.9	22	90	9	68	38	0	0	61	0.96
5784090--5784157	15	4.5	15	75	17	61	44	0	1	54	1.09
5784314--5784372	17	3.6	17	68	9	50	47	0	1	50	1.11
5784318--5784392	32	2.5	29	85	12	114	48	0	2	49	1.15
5784309--5784382	32	2.3	32	95	0	130	48	0	4	47	1.20
5784450--5784490	15	2.9	14	86	13	50	48	7	0	43	1.30
5784465--5784508	15	2.9	15	86	10	54	50	4	0	45	1.22
5784454--5784512	29	2.0	28	81	18	68	50	5	0	44	1.24
5786629--5786814	94	2.0	95	94	1	329	32	14	3	49	1.59
5787785--5787827	8	5.2	8	86	5	50	58	0	0	41	0.98
5787788--5787829	21	2.0	21	85	0	57	54	0	0	45	0.99
5788564--5788613	23	2.1	23	85	7	64	40	0	2	58	1.10
5790317--5790359	20	2.2	20	91	0	68	46	9	2	41	1.48
5791396--5791457	17	3.4	17	70	14	52	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)
5792736--5792807	35	2.1	35	97	0	135	33	6	29	30	1.84
5793856--5793886	3	10.0	3	93	6	53	32	3	0	64	1.09
5794032--5794064	11	2.9	12	82	17	52	66	0	0	33	0.92
5794046--5794137	31	2.9	31	83	8	105	55	0	3	41	1.16
5794033--5794137	33	3.2	33	81	7	110	57	0	2	40	1.14
5794086--5794140	17	3.4	17	69	20	55	54	0	1	43	1.10
5794051--5794152	33	3.2	31	81	8	98	53	0	2	43	1.15
5794355--5794409	24	2.2	25	75	9	60	52	0	0	47	1.00
5795313--5795347	17	1.9	19	88	11	56	48	8	0	42	1.33
5796026--5796077	20	2.7	20	72	21	56	50	0	0	50	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