genome.fa.s4.2.7.7.80.10.50.1000.30.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  30  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)
5796036--5796077	21	2.0	20	86	13	59	54	0	0	45	0.99
5796680--5796721	22	2.0	22	90	4	68	45	0	0	54	0.99
5796732--5796815	25	3.8	21	70	22	55	35	1	0	63	1.03
5805579--5805626	24	2.0	25	87	4	71	41	2	0	56	1.11
5808078--5808423	174	2.0	174	89	1	523	32	26	14	27	1.95
5816385--5816421	15	2.4	16	90	4	58	67	0	0	32	0.91
5818285--5818336	21	2.5	21	81	9	63	34	15	17	32	1.91
5819167--5819211	3	15.0	3	80	0	54	33	8	24	33	1.86
5819167--5819211	6	7.5	6	97	0	63	33	8	24	33	1.86
5826065--5826136	20	3.5	20	86	3	90	40	12	12	34	1.81
5827498--5827539	21	2.0	21	90	9	68	66	0	11	21	1.23
5828848--5828932	45	1.9	44	85	7	118	55	0	0	44	0.99
5829657--5829709	3	17.7	3	100	0	106	66	0	0	33	0.92
5831993--5832056	16	3.9	16	76	19	53	65	0	0	34	0.93
5832003--5832053	21	2.4	21	83	9	59	68	0	0	31	0.90
5832280--5832346	28	2.7	22	72	25	62	38	0	1	59	1.06
5832295--5832340	14	3.3	14	76	11	58	30	0	2	67	1.03
5832762--5832821	31	1.9	31	83	12	79	43	5	0	51	1.23
5833464--5833513	20	2.4	21	80	12	59	34	0	0	66	0.92
5835250--5835315	2	33.0	2	100	0	132	50	0	50	0	1.00
5835812--5835869	27	2.1	28	84	9	75	46	3	1	48	1.29
5835824--5835871	14	3.4	15	71	23	50	45	2	0	52	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5835825--5835882	27	2.2	26	81	12	64	50	1	0	48	1.11
5840098--5840440	129	2.8	122	82	10	412	41	2	1	54	1.22
5840579--5840651	24	2.9	26	75	17	66	64	1	0	34	1.02
5840614--5840663	23	2.2	23	89	7	75	62	0	2	36	1.07
5841163--5841211	17	3.1	17	83	13	52	57	0	2	40	1.10
5841215--5841291	33	2.4	30	77	16	82	54	0	3	41	1.19
5841185--5841293	32	3.2	33	74	22	102	57	0	2	39	1.13
5841241--5841308	16	4.2	15	71	26	50	57	0	1	41	1.08
5841200--5841351	32	5.3	27	70	22	91	58	0	1	38	1.14
5841185--5841341	60	2.7	59	73	18	159	58	0	1	38	1.14
5849539--5849580	18	2.3	19	87	4	59	54	2	0	42	1.13
5849758--5849804	22	2.1	22	84	0	58	48	2	0	48	1.13
5850323--5850370	20	2.4	20	96	0	87	56	4	4	35	1.38
5850568--5850598	16	1.9	16	93	0	53	61	0	0	38	0.96
5851711--5851753	23	1.9	22	90	4	68	58	0	0	41	0.98
5853011--5853065	24	2.3	23	78	9	65	54	0	1	43	1.10
5853009--5853070	31	2.0	30	90	3	97	54	0	1	43	1.09
5853513--5853540	2	14.0	2	100	0	56	50	0	0	50	1.00
5854210--5854253	23	2.0	22	90	4	70	56	0	0	43	0.99
5855306--5855345	20	2.1	18	86	9	53	50	12	10	27	1.72
5856982--5857063	16	5.2	15	78	11	67	58	3	4	32	1.37
5857837--5857885	22	2.3	22	78	3	55	48	2	4	44	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5857869--5857903	17	1.9	18	88	11	54	65	0	0	34	0.93
5857965--5858029	2	35.0	2	76	14	59	46	6	0	47	1.27
5858607--5858646	16	2.4	17	83	8	55	62	0	2	35	1.09
5861094--5861134	16	2.4	18	76	8	50	56	2	2	39	1.26
5862250--5862292	23	1.9	22	86	13	61	58	2	0	39	1.11
5862864--5862896	16	2.1	16	94	0	57	36	21	15	27	1.93
5871281--5871310	8	3.6	8	95	4	51	60	0	0	40	0.97
5871690--5871734	21	2.2	21	84	4	56	51	0	0	48	1.00
5873120--5873148	4	7.2	4	100	0	58	24	0	0	75	0.80
5874476--5874518	3	14.3	3	95	0	77	67	0	2	30	1.03
5876175--5876213	19	2.1	19	85	0	51	48	2	0	48	1.15
5877720--5877763	23	1.9	24	86	9	65	29	4	0	65	1.12
5877725--5877785	16	3.8	16	75	12	61	37	1	0	60	1.07
5878849--5878889	9	4.6	9	90	0	64	68	0	9	21	1.18
5878885--5878951	27	2.6	27	73	4	66	62	0	1	35	1.04
5884017--5884057	2	21.5	2	80	9	50	56	0	0	43	0.99
5884044--5884104	19	3.3	19	71	11	63	50	0	3	45	1.17
5884943--5884979	6	6.2	6	93	0	65	2	16	29	51	1.58
5884937--5884977	18	2.3	18	86	0	55	2	19	24	53	1.57
5887409--5887461	17	3.0	18	83	5	81	50	3	0	45	1.19
5887409--5887482	33	2.2	33	87	4	103	47	6	0	45	1.29
5887572--5887613	21	2.0	21	86	13	59	33	9	0	57	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5887926--5887977	19	2.7	18	74	11	50	30	0	7	61	1.24
5888246--5888283	15	2.8	14	85	14	53	78	0	0	21	0.74
5890613--5890669	28	2.0	29	83	10	73	70	3	1	24	1.13
5890902--5890941	21	1.9	21	90	10	64	57	5	0	37	1.21
5891913--5891982	14	4.7	15	78	18	67	58	0	1	40	1.07
5891913--5891974	19	3.1	19	86	11	72	61	0	0	38	0.96
5892484--5892523	18	2.2	18	90	4	62	35	0	0	65	0.93
5892489--5892569	45	1.9	44	85	12	116	43	0	0	56	0.99
5892537--5892561	12	2.1	12	100	0	50	52	0	0	48	1.00
5892555--5892628	29	2.6	27	79	14	87	37	0	0	62	0.96
5892613--5892646	18	1.9	18	94	5	61	47	0	2	50	1.16
5892964--5893014	24	2.1	24	82	13	61	47	0	0	52	1.00
5893191--5893244	23	2.3	23	78	12	58	68	1	0	29	1.00
5894520--5894552	16	2.1	16	88	5	50	33	15	0	51	1.43
5895708--5895735	6	4.7	6	100	0	56	50	0	0	50	1.00
5896306--5896358	23	2.2	24	86	3	72	69	7	1	20	1.22
5896494--5896522	5	6.0	5	96	4	51	79	0	0	20	0.74
5901283--5901366	32	2.6	32	84	3	116	52	4	2	40	1.35
5901468--5901531	17	3.8	17	72	10	60	37	1	0	60	1.06
5901550--5901598	14	3.4	14	81	10	55	59	16	0	24	1.37
5901819--5901843	4	6.2	4	100	0	50	24	0	0	76	0.80
5906468--5906522	27	2.0	27	85	0	74	52	10	10	25	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5906605--5906709	32	3.4	32	83	7	128	50	7	2	39	1.46
5906617--5906708	28	3.2	28	81	13	105	48	8	3	39	1.50
5909311--5909381	30	2.2	33	85	7	94	43	0	0	56	0.99
5910279--5910317	20	2.0	20	84	0	51	41	0	0	58	0.98
5912017--5912055	16	2.4	16	86	4	51	46	7	5	41	1.55
5914915--5914964	21	2.4	22	76	10	59	58	0	0	42	0.98
5914957--5915033	22	3.5	22	81	10	77	46	12	3	36	1.61
5918090--5918133	21	2.1	21	86	0	61	50	0	0	50	1.00
5918121--5918174	25	2.1	26	82	3	65	46	0	0	53	1.00
5918157--5918187	13	2.4	13	94	0	53	54	0	0	45	0.99
5918675--5918703	2	14.5	2	100	0	58	51	0	0	48	1.00
5921381--5921405	13	1.9	13	100	0	50	28	8	40	24	1.83
5921475--5921573	27	3.7	27	90	4	148	50	20	5	24	1.68
5926438--5926510	35	2.1	35	100	0	146	28	9	13	47	1.74
5926811--5927518	108	6.4	108	75	9	579	24	21	18	35	1.96
5926832--5927518	222	3.1	220	78	8	592	24	21	19	35	1.96
5926811--5927521	330	2.1	330	81	5	824	24	21	18	35	1.96
5929233--5929263	2	15.5	2	100	0	62	48	0	0	51	1.00
5929386--5929429	21	2.0	23	86	8	65	40	0	2	56	1.11
5931485--5931880	198	2.0	198	100	0	792	34	13	13	38	1.84
5932888--5932934	3	16.0	3	95	4	87	65	0	0	34	0.93
5933416--5933510	48	2.0	48	91	0	154	42	7	12	37	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5934226--5934301	16	4.6	17	71	19	63	53	14	3	27	1.58
5934204--5934301	33	3.0	32	76	15	94	51	14	6	28	1.66
5937434--5937486	16	3.4	16	76	2	63	60	16	0	22	1.36
5937434--5937492	16	3.7	15	74	17	57	59	18	0	22	1.38
5942018--5942055	20	1.9	20	88	0	58	28	5	7	57	1.49
5944215--5944260	18	2.6	18	92	0	74	43	2	8	45	1.47
5949544--5949572	14	2.1	14	100	0	58	0	24	0	75	0.80
5949620--5949680	31	2.0	30	84	6	79	57	4	1	36	1.30
5949717--5949853	71	1.9	73	82	11	176	55	13	0	29	1.44
5949840--5949889	22	2.2	21	76	13	55	62	8	0	30	1.24

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