genome.fa.s8.2.7.7.80.10.50.1000.19.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   
          33   

This is table  19  of  33  ( 3942 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)
2806888--2806916	3	9.7	3	100	0	58	31	0	0	68	0.89
2815054--2815103	1	50.0	1	100	0	100	100	0	0	0	0.00
2816549--2816584	19	1.9	19	88	5	56	38	2	0	58	1.13
2818337--2818361	1	25.0	1	100	0	50	100	0	0	0	0.00
2819291--2819324	18	1.9	18	88	5	52	67	0	2	29	1.05
2819791--2819821	15	2.1	15	93	0	53	67	0	0	32	0.91
2820082--2820123	15	2.8	15	80	20	52	52	9	0	38	1.34
2820957--2821055	19	4.9	19	75	16	92	44	1	1	53	1.14
2821663--2821708	1	46.0	1	95	0	83	97	2	0	0	0.15
2822776--2822808	11	2.8	12	86	9	50	81	0	3	15	0.80
2826210--2826253	15	2.8	16	83	12	56	22	0	9	68	1.18
2826217--2826256	17	2.3	18	87	8	57	22	0	10	67	1.20
2826196--2826294	18	5.6	17	70	20	71	24	1	5	69	1.14
2826224--2826293	21	3.3	21	80	4	70	22	0	4	72	1.01
2826244--2826287	16	2.9	14	83	12	52	25	0	2	72	0.96
2833754--2833812	18	2.7	23	70	26	65	45	0	1	52	1.10
2834504--2834608	55	1.9	56	82	5	133	47	0	2	48	1.23
2834603--2834636	10	3.4	10	83	0	50	29	0	2	67	1.05
2834602--2834656	19	2.8	20	78	13	60	36	0	1	61	1.06
2834626--2834671	19	2.4	20	89	7	69	41	2	0	56	1.11
2834665--2834716	19	2.7	19	82	14	63	61	0	1	36	1.07
2834665--2834712	13	3.8	12	78	8	51	62	0	2	35	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2836169--2836264	29	3.3	29	80	7	90	58	2	0	39	1.10
2836240--2836293	22	2.7	21	75	16	60	62	1	0	35	1.06
2836645--2836701	12	4.2	14	78	17	50	61	0	0	38	0.96
2836652--2836714	33	2.0	31	85	11	85	57	0	1	41	1.08
2836671--2836714	16	2.7	17	82	6	56	56	0	2	40	1.11
2837682--2837769	18	4.9	17	75	16	81	46	0	0	53	1.00
2838920--2839011	15	6.3	15	68	20	54	54	1	1	43	1.14
2839329--2839413	29	2.9	30	79	13	95	49	0	0	50	1.00
2840864--2840890	14	1.9	14	100	0	54	33	0	0	66	0.92
2846104--2846165	8	6.9	9	70	26	51	66	0	0	33	0.92
2846103--2846143	16	2.4	18	84	12	59	68	0	0	31	0.90
2846101--2846169	28	2.5	29	81	9	81	66	0	0	33	0.92
2846125--2846163	20	1.9	21	94	5	71	61	0	0	38	0.96
2846551--2846590	2	20.0	2	100	0	80	50	0	0	50	1.00
2847944--2847986	17	2.6	16	82	10	50	48	0	0	51	1.00
2850089--2850113	13	1.9	13	100	0	50	64	0	0	36	0.94
2850089--2850130	6	7.0	6	78	10	50	59	2	0	38	1.10
2853507--2853550	23	2.0	23	86	4	63	56	2	0	40	1.11
2853575--2853615	21	1.9	22	90	5	66	41	0	0	58	0.98
2854673--2854901	111	2.1	111	84	2	291	30	14	3	51	1.57
2857702--2857732	2	15.5	2	100	0	62	48	0	0	51	1.00
2858874--2858917	23	1.9	23	86	9	63	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2858878--2858959	30	2.8	30	87	5	114	41	1	1	56	1.15
2858987--2859040	25	2.2	25	80	6	65	57	3	7	31	1.44
2859727--2859773	23	2.0	23	91	4	76	31	0	0	68	0.90
2859767--2859808	17	2.5	17	88	0	57	52	7	0	40	1.29
2860394--2860422	2	14.5	2	100	0	58	51	0	48	0	1.00
2860905--2860968	32	2.0	33	87	9	96	40	0	1	57	1.08
2861145--2861187	2	21.5	2	90	0	68	51	4	0	44	1.22
2861136--2861189	12	4.5	12	92	0	72	50	9	0	40	1.35
2861337--2861426	38	2.3	37	81	12	101	63	0	5	31	1.17
2863915--2863957	16	2.8	15	86	6	59	34	0	0	65	0.93
2863931--2863976	22	2.1	22	92	8	76	36	2	0	60	1.09
2864133--2864163	2	15.5	2	100	0	62	48	0	0	51	1.00
2864221--2864254	15	2.3	15	89	0	50	47	8	0	44	1.34
2867830--2867902	32	2.3	32	75	15	80	41	0	0	58	0.98
2868186--2868217	3	10.7	3	100	0	64	31	0	0	68	0.90
2868510--2868606	21	4.5	21	71	16	65	45	1	4	49	1.28
2869734--2869758	2	12.5	2	100	0	50	52	0	0	48	1.00
2869886--2869917	10	3.1	11	91	8	50	0	0	81	18	0.70
2870115--2870171	13	4.6	12	79	10	53	54	1	1	42	1.21
2870112--2870178	25	2.6	27	77	15	72	56	2	1	38	1.24
2870133--2870185	24	2.1	25	86	13	74	56	3	3	35	1.35
2872869--2872907	21	1.9	19	90	10	60	51	10	2	35	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2875182--2875242	25	2.4	25	81	8	70	60	1	1	36	1.16
2876733--2876771	5	7.8	5	94	0	69	17	0	2	79	0.84
2881530--2881557	2	14.0	2	100	0	56	50	0	0	50	1.00
2881683--2881722	21	1.9	21	85	10	55	30	2	0	67	1.04
2893577--2893610	16	2.1	16	89	10	52	73	0	0	26	0.83
2894115--2894157	14	3.4	14	76	23	51	41	0	0	58	0.98
2909150--2909174	1	25.0	1	100	0	50	0	100	0	0	0.00
2916759--2916808	14	3.8	14	82	15	70	42	0	0	58	0.98
2916751--2916808	25	2.4	25	82	2	82	44	0	0	55	0.99
2916759--2916816	14	4.3	14	80	14	68	43	0	0	56	0.99
2916754--2916840	39	2.2	39	82	12	106	41	0	0	58	0.98
2928267--2928316	18	2.8	18	80	20	61	50	0	0	50	1.00
2929000--2929032	2	16.5	2	100	0	66	0	48	0	51	1.00
2931167--2931410	88	2.8	85	92	3	409	19	15	10	53	1.71
2934191--2934224	16	2.1	17	88	5	52	64	0	0	35	0.94
2942305--2942347	18	2.3	19	80	15	54	51	0	0	48	1.00
2951468--2951499	15	2.1	15	100	0	64	31	0	34	34	1.58
2953361--2953400	17	2.2	19	86	8	57	32	2	20	45	1.64
2954132--2954160	2	14.5	2	100	0	58	48	0	0	51	1.00
2970524--2970583	23	2.8	20	71	11	57	50	1	0	48	1.11
2985689--2985756	5	14.2	5	73	18	56	39	0	0	60	0.97
2985687--2985771	27	3.1	26	82	14	107	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2985690--2985780	22	4.4	21	71	15	66	40	0	0	59	0.97
2985690--2985826	18	8.2	18	69	23	86	41	0	0	56	1.09
2993374--2993440	33	2.0	34	82	5	82	41	1	2	53	1.25
2995306--2995355	21	2.5	21	84	12	61	38	0	2	60	1.09
2995306--2995346	19	2.2	19	86	8	57	39	0	2	58	1.11
2996280--2996333	20	2.6	20	73	5	54	50	7	0	42	1.30
2997013--2997041	2	14.5	2	100	0	58	0	48	0	51	1.00
2998859--2998903	20	2.2	20	100	0	90	48	0	0	51	1.00
3001233--3001266	16	2.2	15	89	5	50	47	0	2	50	1.16
3001278--3001387	34	3.3	33	72	22	104	39	0	0	60	1.03
3001321--3001360	16	2.6	15	84	7	62	37	0	0	62	0.95
3001282--3001383	5	21.4	5	70	18	58	38	0	0	60	1.03
3002131--3002156	13	2.0	13	100	0	52	38	7	7	46	1.61
3002672--3002715	21	2.1	21	86	0	61	36	2	0	61	1.09
3002682--3002721	21	1.9	21	84	0	53	40	2	0	57	1.12
3003365--3003403	14	2.6	16	84	12	55	38	0	2	58	1.12
3004032--3004073	20	2.0	21	86	13	61	50	2	0	47	1.14
3004464--3004503	6	6.2	6	83	16	53	37	0	0	62	0.95
3005358--3005387	14	2.1	14	93	0	51	60	0	3	36	1.14
3005384--3005420	3	12.3	3	100	0	74	35	0	0	64	0.94
3006078--3006104	2	13.5	2	100	0	54	0	48	0	51	1.00
3006461--3006522	26	2.4	26	84	7	74	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)
3007152--3007185	18	2.0	18	88	11	54	41	0	2	55	1.15
3015406--3015441	2	18.0	2	100	0	72	50	0	50	0	1.00
3016223--3016279	26	2.1	27	83	6	71	43	1	3	50	1.29
3028196--3028228	2	17.0	2	93	6	59	48	0	51	0	1.00
3028591--3028671	35	2.3	35	77	8	85	40	0	1	58	1.06
3028643--3028679	7	5.6	7	84	12	51	40	0	0	59	0.97
3037745--3037841	34	2.9	34	72	20	80	54	0	0	45	0.99
3037904--3037943	18	2.3	18	87	8	57	50	5	10	35	1.58
3044282--3044350	24	2.8	24	76	8	68	57	0	1	40	1.07
3045855--3045895	20	2.0	20	86	9	57	46	0	0	53	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   
          33