genome.fa.s3.2.7.7.80.10.50.1000.18.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  18  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)
2775913--2775947	15	2.2	16	90	5	54	71	0	25	2	1.00
2777110--2777162	3	17.3	3	88	3	79	66	0	3	30	1.10
2781333--2781385	26	2.0	26	89	7	81	43	1	0	54	1.11
2781871--2781937	17	4.1	17	74	12	52	49	1	0	49	1.10
2781893--2781942	16	3.2	15	76	18	57	54	2	0	44	1.11
2781879--2781960	32	2.5	32	86	5	103	47	1	0	51	1.08
2782428--2782465	18	2.1	18	85	9	51	63	7	7	21	1.47
2786960--2787002	19	2.3	19	84	8	52	32	0	0	67	0.91
2786971--2787016	18	2.5	19	83	16	62	28	0	0	71	0.86
2794726--2794750	11	2.3	11	100	0	50	28	0	0	72	0.86
2800715--2800740	1	26.0	1	100	0	52	0	100	0	0	0.00
2806718--2806763	2	23.0	2	90	0	74	0	45	2	52	1.13
2816298--2816322	4	6.2	4	100	0	50	52	0	0	48	1.00
2820114--2820153	20	2.0	21	85	5	55	62	10	0	27	1.27
2820776--2820821	22	2.0	23	87	4	67	58	0	0	41	0.98
2820786--2820833	22	2.2	21	82	17	55	64	0	2	33	1.05
2821119--2821194	13	5.6	14	69	20	54	36	1	3	57	1.25
2821149--2821202	20	2.5	22	85	11	85	38	0	3	57	1.17
2821279--2821342	33	1.9	34	90	3	103	26	1	6	65	1.25
2822061--2822118	16	3.6	16	83	0	80	31	1	3	63	1.21
2822225--2822269	24	1.9	23	81	4	54	35	4	11	48	1.59
2822380--2822422	5	8.6	5	80	19	54	62	0	0	37	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2825079--2825163	16	5.0	17	70	20	70	42	0	1	56	1.07
2825804--2825850	25	1.9	24	82	4	58	51	2	2	44	1.25
2833606--2833636	16	1.9	16	93	0	53	45	3	3	48	1.34
2833607--2833662	22	2.6	21	78	15	62	51	1	1	44	1.22
2833613--2833665	22	2.4	22	84	9	63	50	1	1	45	1.23
2833630--2833682	22	2.4	22	84	6	63	52	1	0	45	1.11
2833637--2833678	15	2.7	15	85	10	50	57	2	0	40	1.12
2838894--2838945	16	3.1	17	78	10	54	61	0	0	38	0.96
2838922--2838969	22	2.3	20	85	7	60	54	2	0	43	1.12
2839045--2839095	26	2.0	26	84	0	66	50	0	0	49	1.00
2839986--2840036	21	2.4	22	90	3	77	50	0	1	47	1.12
2845216--2845246	2	15.5	2	93	0	53	51	3	0	45	1.17
2848836--2848870	2	17.5	2	100	0	70	48	0	0	51	1.00
2850601--2850650	2	25.5	2	85	4	66	2	44	0	54	1.11
2851139--2851169	16	2.0	15	93	6	53	58	0	0	41	0.98
2855621--2855656	19	1.9	18	88	5	54	52	0	0	47	1.00
2856242--2856271	2	15.0	2	100	0	60	50	0	0	50	1.00
2856456--2856516	10	6.1	9	75	22	52	27	0	3	68	1.05
2856456--2856523	33	2.2	32	89	7	104	29	0	2	67	1.05
2856466--2856533	21	3.4	20	80	13	70	32	0	1	66	1.01
2856473--2856534	11	5.5	11	79	9	63	33	0	1	64	1.03
2859293--2859324	6	5.3	6	100	0	64	31	50	0	18	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2862536--2862572	2	19.0	2	88	5	58	45	0	2	51	1.15
2866851--2866947	10	9.3	11	70	20	66	38	0	0	61	0.96
2866851--2866997	5	26.5	6	65	20	54	38	0	0	61	1.01
2866851--2866915	15	4.3	15	74	14	62	35	0	0	64	0.94
2866840--2866882	20	2.3	19	88	8	61	32	0	2	65	1.06
2866857--2866940	23	3.5	26	70	26	69	38	0	0	61	0.96
2866851--2867007	60	2.7	59	72	11	153	38	1	0	59	1.05
2866957--2867010	22	2.4	23	81	9	76	33	3	0	62	1.12
2877176--2877227	27	1.9	27	88	7	79	65	0	0	34	0.93
2877181--2877230	24	2.0	25	85	11	68	66	0	0	34	0.92
2877194--2877261	34	1.9	36	91	8	113	58	1	0	39	1.07
2877161--2877261	37	2.8	35	85	7	114	62	0	0	36	1.02
2877271--2877318	25	2.0	22	84	11	60	56	2	0	41	1.11
2887388--2887434	23	2.0	23	95	0	85	53	6	21	19	1.67
2893032--2893115	41	2.0	41	97	0	159	51	2	9	36	1.48
2902498--2902681	34	5.4	34	85	0	244	26	7	25	40	1.82
2902988--2903050	19	3.3	19	90	0	90	28	17	19	34	1.94
2907114--2907298	34	5.5	34	88	0	264	25	7	26	40	1.82
2910856--2911014	50	3.2	50	93	0	264	30	22	18	28	1.97
2915761--2915791	4	7.8	4	92	0	53	48	3	22	25	1.66
2916122--2916159	2	19.0	2	94	0	67	52	0	0	47	1.00
2916336--2916380	3	14.7	3	95	4	81	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)
2917219--2917268	10	4.5	11	78	16	50	42	0	0	58	0.98
2917221--2917268	12	4.0	12	81	5	53	41	0	0	58	0.98
2917944--2917975	2	16.0	2	100	0	64	50	0	0	50	1.00
2918858--2918922	28	2.4	28	76	7	71	36	0	3	60	1.13
2919077--2919140	30	2.1	30	88	11	96	64	1	0	34	1.03
2919077--2919140	29	2.1	31	88	11	98	64	1	0	34	1.03
2919518--2919564	22	2.2	21	85	11	60	46	0	2	51	1.13
2919523--2919567	18	2.5	18	78	10	56	44	0	2	53	1.13
2919991--2920080	41	2.3	41	84	5	114	43	5	1	50	1.33
2923563--2923594	2	16.0	2	100	0	64	50	0	0	50	1.00
2924688--2924717	2	15.0	2	100	0	60	50	0	0	50	1.00
2925446--2925486	2	20.5	2	94	0	73	53	0	0	46	1.00
2925783--2925869	32	3.0	28	76	14	86	45	0	0	54	1.00
2925811--2925893	14	5.5	15	70	14	55	37	1	0	61	1.04
2925847--2925892	19	2.3	20	85	7	58	28	2	0	69	1.00
2930472--2930503	3	10.7	3	100	0	64	68	0	31	0	0.90
2931210--2931255	24	2.0	23	83	12	58	47	0	0	52	1.00
2931426--2931652	72	3.2	72	83	2	233	38	17	4	39	1.71
2936840--2936911	11	6.8	11	73	17	55	48	0	0	51	1.00
2936826--2936909	41	2.0	41	82	8	100	52	0	0	47	1.00
2936880--2936971	27	3.3	27	81	14	91	52	0	0	47	1.00
2936909--2936973	30	2.3	27	89	7	94	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2937563--2937589	2	13.5	2	100	0	54	51	0	0	48	1.00
2937602--2937690	39	2.5	34	85	10	108	47	2	0	50	1.13
2938236--2938278	17	2.5	17	85	7	52	34	0	4	60	1.17
2938338--2938399	28	2.2	28	82	2	72	56	3	3	37	1.32
2938749--2938818	33	2.1	34	86	7	99	42	1	1	54	1.18
2956265--2956309	22	2.0	22	87	8	65	37	2	4	55	1.32
2959683--2960002	161	2.0	161	99	0	631	40	15	14	30	1.86
2961567--2961624	27	2.1	27	81	15	66	58	3	3	34	1.32
2969508--2969597	27	3.3	27	77	11	69	38	2	0	58	1.10
2969564--2969615	8	6.2	8	85	10	61	30	0	0	69	0.89
2969514--2969606	34	2.8	33	79	19	90	38	2	0	59	1.10
2969559--2969616	7	8.4	7	73	16	50	32	0	0	67	0.91
2970622--2970679	17	3.5	17	73	26	61	53	1	0	44	1.10
2970624--2970678	18	3.3	17	74	25	55	54	1	0	43	1.10
2970896--2970937	14	2.9	14	85	3	57	30	0	0	69	0.89
2971111--2971161	17	2.9	17	85	5	66	33	1	0	64	1.05
2971113--2971153	18	2.3	18	91	0	64	29	2	0	68	1.03
2979288--2979317	5	5.8	5	96	4	51	83	0	0	16	0.65
2980042--2980084	20	2.0	20	86	8	59	53	0	0	46	1.00
2980065--2980117	24	2.1	25	86	10	72	54	0	0	45	0.99
2980041--2980121	31	2.5	32	82	13	96	53	0	0	46	1.00
2981473--2981506	2	17.0	2	100	0	68	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)
2984278--2984380	51	2.0	52	92	1	172	40	14	4	39	1.67
2985595--2985657	28	2.3	27	84	10	83	36	0	6	57	1.24
2985963--2986012	2	25.0	2	87	0	73	48	0	4	48	1.20
2986169--2986306	35	3.9	35	94	0	240	23	33	26	17	1.96
2987090--2987133	3	14.7	3	100	0	88	68	0	0	31	0.90
2988484--2988508	2	12.5	2	100	0	50	48	0	0	52	1.00
2989897--2989925	2	14.5	2	100	0	58	51	0	0	48	1.00
2997470--2997514	17	2.6	19	83	13	53	28	0	0	71	0.87
2998915--2998962	25	2.0	23	84	8	60	31	4	22	41	1.73
3007559--3007598	6	6.5	6	82	5	53	35	0	0	65	0.93

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