genome.fa.s3.2.7.7.80.10.50.1000.19.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  19  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)
3007842--3007907	34	2.0	33	96	3	123	30	19	9	40	1.83
3008727--3008766	17	2.4	16	83	4	53	62	0	0	37	0.95
3009046--3009078	13	2.4	14	90	5	50	72	0	9	18	1.10
3010078--3010152	20	3.8	20	68	26	52	46	0	2	50	1.15
3010170--3010216	13	3.7	13	80	13	53	48	0	2	48	1.13
3010575--3010633	30	2.1	30	84	9	79	47	10	5	37	1.59
3010775--3010830	2	28.0	2	100	0	112	50	0	0	50	1.00
3010990--3011038	25	2.0	25	88	8	73	48	0	4	46	1.20
3011104--3011160	22	2.7	20	79	15	60	50	3	1	43	1.29
3011227--3011254	2	14.0	2	100	0	56	50	0	0	50	1.00
3011689--3011731	21	2.0	22	90	4	70	34	2	0	62	1.08
3012311--3012348	20	1.9	19	85	15	51	50	0	2	47	1.15
3012418--3012506	28	3.2	27	70	7	63	43	0	3	52	1.17
3012539--3012575	3	12.3	3	88	0	56	67	0	2	29	1.04
3012936--3012980	4	11.2	4	95	0	54	66	0	33	0	0.92
3012938--3012985	12	4.0	12	88	0	60	62	0	37	0	0.95
3017689--3017714	2	13.0	2	100	0	52	50	0	0	50	1.00
3021003--3021040	15	2.4	16	82	8	51	44	0	0	55	0.99
3020997--3021058	21	3.0	21	79	11	65	46	1	0	51	1.10
3021032--3021097	35	1.9	34	82	14	82	45	3	0	51	1.16
3021067--3021117	21	2.4	21	78	15	61	52	0	0	47	1.00
3021397--3021428	2	16.5	2	93	6	57	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)
3021646--3021716	23	3.2	23	79	13	78	45	0	0	54	0.99
3021650--3021716	21	3.1	22	81	8	75	44	0	0	55	0.99
3021645--3021721	22	3.3	23	72	17	70	44	0	1	54	1.08
3022437--3022462	3	8.7	3	100	0	52	34	0	0	65	0.93
3023005--3023040	3	12.3	3	94	5	65	30	0	0	69	0.89
3025283--3025320	16	2.4	16	82	13	51	78	2	2	15	0.97
3028261--3028318	23	2.4	24	85	5	82	56	0	0	43	0.99
3029304--3029344	21	1.9	22	90	5	66	58	0	0	41	0.98
3029396--3029447	26	2.0	26	100	0	104	7	26	34	30	1.85
3029398--3029442	14	3.4	14	75	12	58	8	26	33	31	1.87
3030702--3030741	21	1.9	21	90	10	64	52	0	0	47	1.00
3030715--3030765	26	1.9	26	84	4	66	60	0	0	39	0.97
3030739--3030777	20	2.0	20	100	0	78	61	0	0	38	0.96
3033279--3033313	5	7.0	5	100	0	70	40	0	0	60	0.97
3033820--3033915	38	2.6	36	80	6	95	43	2	15	38	1.59
3034283--3034307	13	1.9	13	100	0	50	32	8	16	44	1.76
3038599--3038702	38	2.7	38	79	5	120	35	7	22	34	1.83
3039122--3039151	11	2.6	12	94	5	53	23	0	0	76	0.78
3046422--3046478	27	2.1	27	83	0	69	42	26	8	22	1.83
3046623--3046718	29	3.3	28	83	2	111	23	28	15	32	1.95
3046812--3046836	2	12.5	2	100	0	50	52	48	0	0	1.00
3049382--3049422	21	2.0	21	85	0	55	56	2	0	41	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3049473--3049568	31	3.1	31	75	10	81	52	1	1	45	1.14
3049515--3049618	55	1.9	55	82	7	131	45	2	0	51	1.16
3049559--3049608	14	3.3	15	76	18	50	42	2	0	56	1.11
3049560--3049607	21	2.2	21	85	10	62	39	2	0	58	1.10
3049509--3049617	16	7.0	15	74	14	62	44	2	0	52	1.15
3052512--3052569	29	2.0	29	96	0	107	31	6	32	29	1.84
3053733--3053766	2	17.0	2	100	0	68	50	0	0	50	1.00
3057450--3057504	29	2.0	27	82	13	67	52	0	0	47	1.00
3057482--3057516	17	2.0	17	88	5	52	57	0	0	42	0.99
3057809--3057889	21	3.8	22	81	14	89	49	0	0	50	1.00
3057931--3058115	6	31.0	6	65	22	54	49	2	0	48	1.13
3057963--3058115	21	6.9	22	69	22	70	49	0	0	50	1.05
3057908--3058012	38	3.1	33	73	20	92	47	3	0	48	1.20
3057974--3058056	44	1.9	44	85	7	116	48	1	0	50	1.08
3057964--3058115	43	3.4	42	75	19	123	49	0	0	50	1.05
3058031--3058113	42	2.0	43	83	7	107	51	0	0	48	1.00
3057931--3058115	11	15.5	12	67	22	54	49	2	0	48	1.13
3058037--3058113	21	3.6	21	80	16	79	53	0	0	46	1.00
3058037--3058115	36	2.3	34	82	6	95	53	0	0	46	1.00
3062753--3062784	2	16.0	2	100	0	64	0	50	0	50	1.00
3065275--3065321	18	2.9	16	76	14	51	57	0	2	40	1.11
3065316--3065380	16	4.0	16	70	21	55	56	0	0	43	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3065317--3065396	32	2.6	32	84	7	94	57	0	1	41	1.07
3065316--3065370	16	3.4	17	76	16	62	58	0	0	41	0.98
3075331--3075411	39	2.0	41	81	9	96	45	3	3	46	1.38
3075413--3075470	26	2.2	26	84	6	71	51	1	1	44	1.21
3078714--3078746	8	4.2	8	92	7	50	0	6	3	90	0.52
3078710--3078739	14	2.2	14	94	5	53	0	10	0	90	0.47
3097177--3097202	2	13.0	2	100	0	52	50	0	0	50	1.00
3105764--3105800	2	18.5	2	100	0	74	51	48	0	0	1.00
3111135--3111180	21	2.2	21	88	0	65	65	8	4	21	1.38
3111143--3111184	21	2.0	21	100	0	84	57	9	4	28	1.51
3116176--3116231	26	2.1	27	87	9	80	50	0	1	48	1.11
3117178--3117240	27	2.4	27	75	15	69	60	0	0	39	0.97
3117153--3117236	19	4.8	19	75	15	74	60	0	1	38	1.04
3125658--3125690	16	2.1	16	100	0	66	30	12	27	30	1.92
3130231--3130275	23	2.0	23	91	4	74	40	15	15	28	1.88
3132693--3132775	42	2.0	41	90	6	132	44	22	9	22	1.82
3135120--3135230	42	2.7	39	74	13	98	54	0	0	45	1.06
3135148--3135186	18	2.1	17	86	13	51	38	0	0	61	0.96
3135178--3135276	48	2.1	48	80	14	107	56	2	0	41	1.11
3135714--3135747	17	2.0	17	88	0	50	58	0	0	41	0.98
3137451--3137501	19	2.5	20	84	12	61	47	0	0	52	1.00
3140516--3140553	19	2.0	19	100	0	76	36	5	10	47	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3143947--3143984	6	6.5	6	90	3	51	18	0	60	21	1.36
3143947--3143984	12	3.2	12	88	3	60	18	0	60	21	1.36
3146555--3146582	13	2.2	13	100	0	56	17	14	21	46	1.84
3149938--3149991	2	27.5	2	90	3	83	48	1	1	48	1.23
3157844--3157931	37	2.4	37	77	12	92	47	0	0	52	1.00
3157847--3157920	21	3.4	22	75	17	59	43	0	0	56	0.99
3160425--3160452	2	14.0	2	100	0	56	50	0	0	50	1.00
3166754--3166805	25	2.0	26	85	7	70	38	3	0	57	1.17
3169857--3169887	2	15.5	2	93	0	53	48	48	3	0	1.17
3181504--3181577	3	24.7	3	94	0	121	63	0	4	32	1.13
3185501--3185545	18	2.3	18	85	11	54	57	0	2	40	1.11
3185518--3185565	20	2.5	20	86	6	64	58	0	0	41	0.98
3186025--3186091	32	2.1	32	91	0	107	46	4	5	43	1.48
3185977--3186139	80	2.0	80	91	0	263	43	7	7	41	1.62
3186057--3186151	48	2.0	48	89	0	145	41	7	9	42	1.65
3189173--3189231	24	2.3	26	86	11	79	44	3	0	52	1.17
3189485--3189542	30	2.0	29	86	3	80	56	0	0	43	0.99
3190692--3190766	33	2.3	33	97	0	141	45	42	12	0	1.41
3190696--3190763	30	2.3	30	92	0	109	47	44	8	0	1.34
3194795--3194914	61	2.0	61	98	0	231	26	21	14	37	1.92
3201900--3201965	29	2.3	29	81	0	69	48	4	4	42	1.44
3204799--3204842	2	22.0	2	100	0	88	50	0	50	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3207192--3207225	17	2.0	17	88	0	50	0	17	0	82	0.67
3211509--3211576	31	2.2	31	80	10	77	32	4	2	60	1.32
3213320--3213359	21	1.9	22	85	10	57	52	2	2	42	1.28
3213895--3213961	22	3.0	21	77	12	64	55	0	0	44	0.99
3213895--3213948	21	2.5	22	85	8	67	57	0	0	42	0.98
3213884--3213961	21	3.3	23	72	16	63	53	0	0	46	1.00
3226439--3226480	16	2.6	17	82	17	54	50	0	0	50	1.00
3226524--3226569	13	3.5	13	79	5	56	56	0	0	43	0.99
3226524--3226581	27	2.1	27	83	3	71	60	0	0	39	0.97
3226638--3226697	23	2.5	24	84	13	79	53	0	0	46	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   32