genome.fa.s40.2.7.7.80.10.50.1000.18.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: Scaffold40
Parameters: 2 7 7 80 10 50 1000
Length:  3440810

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   

This is table  18  of  24  ( 2833 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)
2325008--2325039	7	4.7	7	96	3	57	9	43	31	15	1.78
2325962--2325986	13	1.9	13	100	0	50	52	0	0	48	1.00
2326006--2326030	13	1.9	13	100	0	50	56	0	0	44	0.99
2330678--2330703	3	8.7	3	100	0	52	69	0	0	30	0.89
2332618--2332651	3	11.3	3	93	0	59	32	2	0	64	1.08
2333121--2333160	13	3.2	13	80	20	57	50	0	0	50	1.00
2333412--2333446	16	2.2	16	89	0	52	22	11	17	48	1.79
2333451--2333481	16	2.0	16	93	6	55	19	16	25	38	1.92
2333482--2333548	16	4.2	16	80	0	71	25	14	14	44	1.84
2333483--2333544	32	1.9	32	83	0	79	27	16	11	45	1.81
2334634--2334688	12	4.2	13	73	13	51	54	0	0	45	0.99
2339336--2339506	93	1.8	92	90	3	272	44	13	11	30	1.79
2339426--2339491	20	3.3	20	80	0	78	42	12	10	34	1.77
2343640--2343691	16	3.2	16	86	2	68	28	11	13	46	1.78
2343684--2343757	6	13.3	6	77	11	54	48	0	0	51	1.00
2343685--2343763	5	15.8	5	73	16	58	50	0	0	49	1.00
2343685--2343764	15	5.3	15	77	14	76	50	0	0	50	1.00
2344117--2344165	16	3.1	16	77	13	57	38	0	0	61	0.96
2344357--2344383	13	2.1	13	100	0	54	70	0	0	29	0.88
2344356--2344389	13	2.9	11	84	16	50	64	0	0	35	0.94
2344715--2344744	2	15.0	2	100	0	60	50	0	0	50	1.00
2345943--2345977	2	17.5	2	100	0	70	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2346521--2346550	8	3.8	8	95	0	51	20	0	0	80	0.72
2346953--2346998	3	15.3	3	100	0	92	67	0	0	32	0.91
2350132--2350169	19	2.0	19	89	0	58	44	5	10	39	1.61
2357031--2357061	2	15.5	2	100	0	62	48	0	51	0	1.00
2357254--2357349	36	2.7	35	74	16	90	54	1	0	44	1.07
2357228--2357321	26	3.7	27	72	16	69	59	1	0	39	1.04
2357241--2357347	20	5.1	20	71	18	56	57	0	0	42	1.05
2357274--2357390	36	3.3	36	73	19	104	55	1	0	42	1.10
2357267--2357352	22	3.6	22	72	18	66	54	1	0	44	1.07
2357267--2357357	26	3.8	24	72	22	66	54	1	0	43	1.07
2357222--2357370	64	2.3	65	79	14	175	59	0	0	39	1.02
2357209--2357390	64	2.8	64	80	8	172	57	1	0	40	1.10
2357722--2357783	15	4.3	14	82	12	72	41	0	0	58	0.98
2357722--2357783	28	2.1	29	88	5	90	41	0	0	58	0.98
2357722--2357771	13	3.6	13	82	12	64	38	0	0	62	0.96
2357892--2357942	20	2.5	20	75	12	52	39	0	0	60	0.97
2358158--2358198	17	2.3	18	84	12	50	58	4	0	36	1.20
2358830--2358896	25	2.8	24	82	13	75	59	2	0	37	1.13
2359587--2359626	20	2.1	19	85	4	53	55	2	5	37	1.35
2359727--2359776	26	1.9	26	87	0	73	68	0	2	30	1.01
2360017--2360057	21	1.9	22	95	5	75	56	14	0	29	1.39
2360379--2360424	22	2.1	22	84	8	58	36	2	2	58	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2361181--2361234	22	2.5	22	77	20	60	48	1	0	50	1.11
2361906--2361949	18	2.4	19	84	3	54	52	2	0	45	1.13
2367486--2367536	24	2.1	24	86	13	70	43	0	0	56	0.99
2367489--2367542	13	4.3	13	77	13	51	40	0	0	59	0.98
2367982--2368035	22	2.5	21	80	16	74	37	22	11	29	1.89
2368033--2368199	34	4.9	34	85	0	210	41	26	7	25	1.81
2370866--2370936	36	2.0	36	100	0	142	40	19	14	25	1.89
2372642--2372857	34	6.4	33	79	8	229	41	24	7	26	1.81
2372642--2372857	67	3.2	67	82	2	263	41	24	7	26	1.81
2372642--2372857	101	2.1	101	84	2	299	41	24	7	26	1.81
2375010--2375119	53	2.1	54	96	1	204	39	8	9	43	1.66
2375010--2375129	54	2.2	53	91	1	186	38	10	9	41	1.72
2377072--2377114	13	3.2	13	81	12	50	53	0	0	46	1.00
2377383--2377428	21	2.1	22	84	4	58	52	6	0	41	1.27
2378161--2378192	11	2.8	11	95	4	55	34	0	0	65	0.93
2383153--2383203	23	2.2	23	85	0	66	56	0	1	41	1.10
2388353--2388378	4	6.5	4	100	0	52	23	0	0	76	0.78
2391435--2391474	20	2.1	20	86	9	57	40	0	0	60	0.97
2392586--2392681	37	2.6	34	82	14	95	53	0	1	45	1.07
2393558--2393585	2	14.0	2	100	0	56	50	0	0	50	1.00
2394190--2394235	3	15.3	3	95	0	83	32	2	0	65	1.05
2394449--2394495	20	2.3	21	86	13	64	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2394589--2394635	2	25.0	2	81	12	55	51	2	0	46	1.13
2396765--2396814	2	25.5	2	87	4	75	50	2	0	48	1.12
2397221--2397287	33	2.0	33	82	0	80	68	4	1	25	1.17
2398070--2398104	17	2.1	17	88	0	52	37	2	22	37	1.69
2398637--2398678	22	1.9	22	90	0	66	40	14	7	38	1.73
2399252--2399295	21	2.0	22	86	8	63	59	2	0	38	1.10
2399632--2399662	2	15.5	2	100	0	62	51	0	48	0	1.00
2400118--2400169	21	2.4	21	81	9	61	44	0	1	53	1.11
2401285--2401336	17	3.1	18	75	10	56	46	0	1	51	1.12
2401620--2401660	21	2.0	21	86	13	59	39	0	0	60	0.96
2404888--2404919	2	16.0	2	100	0	64	50	0	0	50	1.00
2405343--2405379	2	18.5	2	94	0	65	45	0	2	51	1.15
2411152--2411185	2	17.0	2	100	0	68	50	0	50	0	1.00
2411939--2411987	12	4.2	12	78	14	50	44	0	2	53	1.12
2411915--2411996	24	3.5	25	74	22	79	40	0	1	58	1.06
2411913--2412008	25	3.5	25	70	23	77	37	0	1	61	1.03
2411908--2412033	19	6.6	20	71	17	81	38	0	0	60	1.03
2412629--2412749	8	15.9	8	66	22	55	58	0	1	38	1.14
2412632--2412755	39	3.2	38	73	13	103	58	0	1	38	1.13
2413164--2413212	20	2.6	19	75	9	55	73	0	8	18	1.07
2413599--2413677	20	3.8	21	73	17	76	32	1	5	60	1.26
2413573--2413687	21	5.8	19	71	20	85	33	0	3	62	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2413741--2413783	17	2.4	19	85	11	56	37	0	0	62	0.95
2413768--2413827	31	1.9	31	86	3	84	50	1	1	46	1.21
2417897--2418130	127	1.8	126	87	4	346	30	13	19	36	1.90
2419548--2419604	21	2.6	21	78	13	62	68	0	29	1	1.00
2419549--2419592	21	2.1	21	87	4	63	65	0	31	2	1.05
2420872--2420902	2	15.5	2	100	0	62	48	0	51	0	1.00
2428693--2428727	16	2.2	16	89	0	52	42	2	0	54	1.15
2428824--2428876	17	3.3	17	79	7	58	56	0	0	43	0.99
2429237--2429266	15	1.9	16	93	6	53	56	0	0	43	0.99
2434101--2434154	18	3.0	18	81	5	56	37	0	0	62	0.95
2435358--2435400	11	3.7	11	77	22	52	25	2	0	72	0.97
2435352--2435408	24	2.4	24	83	13	82	29	1	0	68	1.00
2435358--2435402	12	3.8	12	80	13	58	26	2	0	71	0.98
2435352--2435408	12	4.9	12	75	14	57	29	1	0	68	1.00
2435929--2435992	25	2.5	26	89	5	94	60	0	0	39	0.97
2435972--2436033	2	32.0	2	76	12	58	58	1	0	40	1.08
2435935--2436044	39	3.1	37	80	13	124	62	0	0	36	1.01
2435935--2436036	8	12.4	8	73	20	59	61	0	0	37	1.03
2436175--2436205	2	15.5	2	100	0	62	48	0	0	51	1.00
2436317--2436365	17	2.9	16	84	6	62	61	0	0	38	0.96
2436318--2436371	16	3.3	16	86	2	63	55	0	1	42	1.10
2437203--2437258	16	3.6	15	76	13	51	62	3	1	32	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2437702--2437735	13	2.7	13	86	4	52	55	8	0	35	1.31
2441782--2441818	18	2.1	18	90	10	58	43	5	2	48	1.40
2442364--2442437	38	1.9	38	97	0	139	35	16	0	48	1.46
2442700--2442740	2	20.5	2	94	0	73	48	0	0	51	1.00
2443082--2443130	22	2.2	22	85	7	64	48	0	2	48	1.12
2443575--2443630	21	2.7	20	86	8	85	46	0	1	51	1.11
2443814--2443839	5	5.2	5	100	0	52	61	0	0	38	0.96
2444834--2444878	19	2.5	17	85	7	63	57	0	0	42	0.98
2445678--2445741	28	2.4	27	77	12	69	15	17	4	62	1.49
2446723--2446757	2	17.5	2	100	0	70	48	0	0	51	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