genome.fa.s3.2.7.7.80.10.50.1000.15.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  15  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)
2228208--2228257	25	2.0	25	92	0	82	30	30	12	28	1.92
2230105--2230134	13	2.2	14	94	5	53	90	0	10	0	0.47
2230105--2230134	14	2.1	14	93	0	51	90	0	10	0	0.47
2231002--2231044	15	2.6	17	85	10	54	53	0	0	46	1.00
2231006--2231045	17	2.3	19	79	16	50	52	0	0	47	1.00
2231254--2231284	4	7.8	4	92	0	53	74	0	3	22	0.96
2232229--2232254	13	2.0	13	100	0	52	61	7	0	30	1.24
2232218--2232264	21	2.3	20	85	7	67	65	4	0	29	1.11
2232284--2232343	30	2.1	29	81	12	70	53	0	0	46	1.00
2233949--2234005	26	2.1	27	81	9	64	45	3	0	50	1.18
2234370--2234442	19	3.7	19	78	14	69	57	1	0	41	1.07
2234713--2234741	3	9.7	3	100	0	58	68	0	0	31	0.89
2243460--2243497	17	2.2	17	100	0	76	28	23	26	21	1.99
2246140--2246188	24	2.0	24	96	0	89	48	4	10	36	1.56
2246550--2246579	2	15.0	2	100	0	60	0	50	0	50	1.00
2248217--2248261	23	1.9	23	81	4	54	31	0	6	62	1.21
2249669--2249717	5	10.2	5	80	12	50	63	0	0	36	0.95
2250055--2250093	7	5.6	7	85	11	53	71	0	0	28	0.86
2250674--2250728	20	2.6	21	85	5	67	65	0	0	34	0.93
2250698--2250732	15	2.2	16	90	5	54	62	0	0	37	0.95
2250683--2250751	34	2.1	32	86	8	93	59	1	0	39	1.06
2251401--2251444	19	2.3	19	80	0	52	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)
2251441--2251478	17	2.2	18	86	9	53	39	2	0	57	1.12
2255859--2255893	6	6.0	6	86	6	54	0	17	0	82	0.66
2255859--2255894	17	2.1	17	90	10	56	0	19	0	80	0.71
2256145--2256200	14	3.8	15	81	11	71	21	0	5	73	1.03
2256149--2256209	29	2.1	29	84	6	79	22	0	4	72	1.04
2256154--2256314	75	2.1	74	81	3	178	29	1	6	61	1.32
2256501--2256551	18	2.8	18	72	0	57	66	0	0	33	0.92
2256837--2256878	20	2.1	21	91	8	70	33	0	0	66	0.92
2256843--2256883	19	2.2	19	86	8	57	34	0	2	63	1.08
2256881--2256939	20	3.0	20	73	11	59	47	0	0	52	1.00
2262621--2262670	12	4.0	13	74	7	50	44	0	0	56	0.99
2265677--2265706	2	15.0	2	100	0	60	50	0	0	50	1.00
2265757--2265789	16	2.0	17	94	5	59	66	0	0	33	0.92
2267163--2267208	22	2.0	23	84	12	60	41	2	0	56	1.11
2267322--2267401	28	2.9	28	79	5	92	60	0	0	40	0.97
2267342--2267391	16	2.7	18	82	17	59	58	0	0	42	0.98
2267336--2267376	16	2.5	17	92	4	66	60	0	0	39	0.96
2267363--2267460	31	3.3	31	83	12	118	52	0	1	46	1.07
2271571--2271605	2	17.5	2	93	0	61	51	0	2	45	1.16
2273708--2273738	2	15.5	2	100	0	62	48	0	0	51	1.00
2274377--2274435	15	3.9	15	77	14	59	52	0	0	47	1.00
2278672--2278703	15	2.0	17	88	11	50	37	9	0	53	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2279491--2279524	13	2.5	13	90	4	50	0	11	0	88	0.52
2283240--2283278	14	2.8	14	84	0	51	35	0	0	64	0.94
2283262--2283343	36	2.3	35	77	10	94	53	0	0	46	1.00
2284405--2284446	20	2.0	21	90	4	68	61	0	0	38	0.96
2284414--2284460	19	2.5	20	76	13	55	65	0	0	34	0.93
2284497--2284566	20	3.3	20	76	15	70	41	0	0	58	0.98
2284466--2284533	32	2.2	32	87	10	97	42	0	1	55	1.08
2284539--2284604	13	5.0	13	71	23	57	46	0	1	51	1.10
2284495--2284571	10	7.2	11	76	12	63	42	0	0	57	0.99
2284400--2284629	29	8.2	29	68	18	96	46	0	1	51	1.09
2284467--2284589	41	2.9	44	73	17	118	42	0	1	56	1.09
2284986--2285027	2	22.0	2	90	9	70	52	0	47	0	1.00
2288300--2288336	2	18.5	2	100	0	74	48	0	0	51	1.00
2289818--2289843	2	13.0	2	100	0	52	50	0	50	0	1.00
2293168--2293300	67	2.0	67	96	0	248	30	16	7	45	1.75
2293745--2293783	19	2.1	19	100	0	78	25	30	7	35	1.84
2310605--2310653	22	2.2	22	77	0	53	48	0	2	48	1.12
2311358--2311382	13	1.9	13	100	0	50	80	0	8	12	0.92
2315900--2315945	17	2.4	20	75	20	53	39	0	6	54	1.26
2321187--2321211	6	4.2	6	100	0	50	0	52	16	32	1.44
2321282--2321311	2	15.0	2	100	0	60	50	0	50	0	1.00
2323396--2323445	23	2.2	23	82	7	57	32	16	4	48	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2323786--2323819	2	17.0	2	87	0	50	47	2	2	47	1.32
2325334--2325384	20	2.4	21	75	15	52	49	3	1	45	1.32
2325477--2325519	22	2.0	20	91	8	68	37	0	2	60	1.10
2325463--2325522	22	2.7	22	73	21	61	38	1	3	56	1.26
2326068--2326109	12	3.6	12	78	18	52	47	0	0	52	1.00
2326064--2326108	23	2.0	23	90	0	72	51	0	0	48	1.00
2326063--2326126	29	2.1	29	85	5	83	46	1	0	51	1.10
2328999--2329043	22	2.0	22	91	8	74	48	0	0	51	1.00
2329004--2329050	23	2.0	23	88	8	69	51	0	0	48	1.00
2329242--2329290	19	2.3	20	80	16	55	48	0	4	46	1.20
2329254--2329296	19	2.3	19	91	0	68	55	0	0	44	0.99
2329300--2329325	8	3.2	8	100	0	52	65	0	0	34	0.93
2329339--2329398	27	2.3	26	86	11	79	56	0	0	43	0.99
2332224--2332275	19	2.7	21	80	19	60	55	0	0	44	0.99
2344048--2344105	20	2.9	19	76	20	57	53	0	0	46	1.00
2344804--2344839	11	3.5	11	82	17	51	47	0	0	52	1.00
2344948--2345014	19	3.6	19	74	11	66	62	0	0	37	0.95
2347730--2347758	14	2.1	14	100	0	58	13	13	27	44	1.82
2352377--2352417	2	20.5	2	89	0	64	46	0	0	53	1.00
2352818--2352843	13	2.0	13	100	0	52	76	0	15	7	0.99
2353165--2353198	13	2.8	12	82	8	50	58	0	0	41	0.98
2354107--2354234	16	8.9	15	68	22	80	54	1	2	41	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2354148--2354234	15	5.5	15	75	18	70	55	1	3	40	1.24
2354433--2354480	22	2.2	22	84	0	60	60	2	4	33	1.27
2355619--2355909	143	2.0	143	95	0	528	54	16	6	21	1.65
2355732--2355777	16	2.9	16	73	20	51	65	13	0	21	1.26
2360252--2360302	26	1.9	27	88	4	77	27	1	0	70	0.98
2360246--2360305	27	2.4	26	78	13	72	28	3	0	68	1.05
2360726--2360755	2	15.0	2	100	0	60	50	0	0	50	1.00
2361449--2361473	4	6.2	4	100	0	50	48	0	0	52	1.00
2361608--2361651	21	2.1	22	87	8	65	29	0	0	70	0.88
2366467--2366509	16	2.7	15	75	10	50	46	0	0	53	1.00
2366468--2366531	33	2.0	33	84	9	87	43	1	0	54	1.09
2366514--2366559	24	1.9	23	83	16	58	30	0	0	69	0.89
2366794--2366818	4	6.2	4	100	0	50	24	0	0	76	0.80
2367849--2367890	22	2.0	22	86	9	61	30	0	0	69	0.89
2367856--2367899	20	2.2	20	84	12	54	31	2	0	65	1.05
2374068--2374124	28	2.0	28	82	0	69	38	8	10	42	1.71
2374827--2374870	22	2.1	21	87	8	63	38	11	6	43	1.67
2376358--2376402	16	2.9	15	84	12	56	42	0	0	57	0.98
2378657--2378702	20	2.3	20	88	11	76	52	0	0	47	1.00
2378660--2378706	19	2.5	19	93	3	78	51	0	0	48	1.00
2379892--2379918	2	13.5	2	100	0	54	51	0	0	48	1.00
2380584--2380650	34	2.0	34	85	5	91	53	1	8	35	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2381935--2382010	37	2.1	37	83	14	95	51	2	0	46	1.15
2383187--2383253	19	3.3	19	73	15	53	61	2	0	35	1.12
2383187--2383246	23	2.5	22	76	12	57	61	1	0	36	1.06
2389117--2389154	11	3.2	12	85	11	51	42	0	0	57	0.98
2389117--2389154	6	6.3	6	84	9	51	42	0	0	57	0.98
2389121--2389154	17	1.9	18	88	5	52	44	0	0	55	0.99
2389395--2389435	18	2.3	18	84	12	50	51	0	2	46	1.14
2389673--2389716	22	2.1	22	87	8	65	38	9	6	45	1.63
2391339--2391371	5	7.0	5	93	6	52	42	0	0	57	0.98
2392559--2392606	24	2.0	24	83	4	60	54	2	6	37	1.38

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