genome.fa.s8.2.7.7.80.10.50.1000.17.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  17  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)
2329238--2329271	9	3.9	9	92	7	61	79	0	11	8	0.94
2329209--2329260	22	2.5	21	90	6	79	78	0	15	5	0.92
2329241--2329270	8	3.6	8	95	4	51	80	0	10	10	0.92
2329339--2329392	27	2.0	27	82	10	65	33	0	1	64	1.04
2329436--2329496	19	3.2	18	79	9	68	34	3	3	59	1.30
2331344--2331375	7	4.7	7	92	7	57	71	0	0	28	0.86
2336754--2336809	26	2.2	25	87	3	76	39	0	3	57	1.16
2341084--2341117	15	2.2	16	89	5	52	76	0	0	23	0.79
2341701--2341764	29	2.2	29	85	2	83	53	0	3	43	1.16
2342915--2342983	30	2.3	30	80	9	79	53	2	0	43	1.15
2343547--2343601	29	1.9	28	88	3	83	43	0	0	56	0.99
2343547--2343598	13	3.8	13	73	14	50	42	0	0	57	0.98
2343605--2343645	16	2.5	17	77	22	52	41	0	0	58	0.98
2348368--2348403	18	1.9	20	88	11	58	47	0	0	52	1.00
2348730--2348809	30	2.5	30	80	9	88	43	1	1	53	1.16
2349429--2349489	20	3.0	21	74	11	65	42	3	0	54	1.17
2350497--2350550	19	3.2	16	78	19	56	68	1	0	29	1.00
2351286--2351333	19	2.5	19	86	10	62	39	0	2	58	1.10
2351780--2351827	20	2.7	17	74	20	53	35	0	0	64	0.94
2352436--2352468	2	16.5	2	100	0	66	51	0	48	0	1.00
2372889--2372929	21	1.9	22	85	5	57	24	4	14	56	1.58
2380172--2380201	2	15.0	2	100	0	60	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2388196--2388227	3	10.7	3	100	0	64	31	0	0	68	0.90
2401652--2401678	2	13.5	2	100	0	54	0	48	0	51	1.00
2403004--2403036	2	16.5	2	100	0	66	51	0	0	48	1.00
2410261--2410297	2	18.5	2	100	0	74	51	0	0	48	1.00
2413901--2413941	15	2.7	16	85	11	59	36	0	2	60	1.10
2414013--2414057	17	2.6	18	82	10	58	46	0	2	51	1.13
2414603--2414628	2	13.0	2	100	0	52	50	0	0	50	1.00
2415308--2415337	2	15.0	2	100	0	60	0	50	0	50	1.00
2418194--2418221	2	14.0	2	100	0	56	50	0	0	50	1.00
2419069--2419096	2	14.0	2	100	0	56	50	0	0	50	1.00
2428524--2428594	25	2.7	27	76	8	83	66	4	0	29	1.11
2429740--2429838	29	3.2	28	76	18	108	43	2	1	53	1.19
2431174--2431237	22	3.0	22	79	9	69	53	1	0	45	1.10
2431167--2431232	21	3.2	21	77	12	57	56	1	0	42	1.08
2435740--2435769	2	15.0	2	100	0	60	50	0	0	50	1.00
2435991--2436021	2	16.0	2	93	6	55	51	0	0	48	1.00
2440003--2440053	2	25.5	2	100	0	102	49	0	0	50	1.00
2444298--2444337	2	20.0	2	94	0	71	47	0	2	50	1.14
2447091--2447141	16	3.2	16	78	10	61	37	3	1	56	1.29
2447085--2447129	16	2.8	16	83	6	56	40	2	4	53	1.33
2448594--2448621	14	2.0	14	100	0	56	35	0	7	57	1.26
2451301--2451339	2	19.5	2	100	0	78	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)
2453511--2453543	14	2.5	14	90	9	52	33	0	0	66	0.92
2464474--2464514	3	13.7	3	94	0	73	63	0	34	2	1.08
2469511--2469549	20	2.0	20	100	0	78	33	10	0	56	1.33
2470262--2470295	17	1.9	18	94	5	61	47	2	0	50	1.16
2474791--2474825	9	3.9	9	92	0	52	5	14	34	45	1.68
2476979--2477016	2	19.0	2	100	0	76	50	0	0	50	1.00
2480334--2480366	14	2.4	14	94	0	57	51	0	0	48	1.00
2483401--2483492	43	2.1	43	97	0	175	31	16	8	43	1.78
2486556--2486659	27	3.9	27	88	0	154	11	24	30	33	1.91
2492490--2492536	2	23.5	2	100	0	94	51	0	48	0	1.00
2501411--2501440	3	10.0	3	100	0	60	66	0	33	0	0.92
2502028--2502079	2	26.0	2	100	0	104	50	0	50	0	1.00
2502124--2502150	4	6.8	4	100	0	54	51	0	22	25	1.48
2508822--2508880	22	2.5	24	81	10	61	40	1	1	55	1.20
2510066--2510128	21	2.9	21	73	4	54	63	0	0	36	0.95
2511079--2511294	102	2.1	101	85	6	294	28	7	23	40	1.81
2511078--2511296	34	6.5	33	81	5	233	27	7	23	41	1.81
2515707--2515923	34	6.4	33	83	5	263	25	7	25	40	1.82
2515707--2515921	102	2.1	101	88	1	322	26	7	25	40	1.83
2522260--2522292	17	1.9	17	93	0	57	72	0	0	27	0.85
2525682--2525707	13	2.0	13	100	0	52	7	0	23	69	1.14
2526908--2526940	2	16.5	2	93	0	57	48	0	3	48	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2531174--2531207	14	2.4	14	86	13	52	58	0	0	41	0.98
2536442--2536499	26	2.3	26	84	3	73	34	12	12	41	1.79
2537797--2537845	8	6.5	8	80	15	52	69	0	0	30	0.89
2537779--2537845	29	2.4	27	75	15	66	65	0	0	34	0.93
2539586--2539627	15	2.9	14	83	16	50	54	2	0	42	1.13
2542735--2542763	2	14.5	2	100	0	58	48	0	0	51	1.00
2543702--2543741	14	2.8	14	84	3	53	42	0	2	55	1.13
2543697--2543776	5	16.4	5	70	14	51	37	1	2	58	1.19
2543697--2543776	9	8.2	10	69	13	51	37	1	2	58	1.19
2543708--2543761	24	2.3	24	83	3	65	37	1	1	59	1.19
2544359--2544413	22	2.6	22	77	11	53	67	7	0	25	1.16
2545857--2545893	2	18.5	2	100	0	74	51	0	0	48	1.00
2548221--2548250	8	3.8	8	100	0	60	80	0	0	20	0.72
2548263--2548290	2	14.0	2	100	0	56	0	50	0	50	1.00
2548588--2548616	3	9.7	3	100	0	58	68	0	31	0	0.89
2552440--2552477	19	2.0	19	90	10	60	34	0	0	65	0.93
2556219--2556260	17	2.5	17	84	0	57	38	0	4	57	1.20
2557618--2557679	30	2.1	29	88	8	90	50	0	0	50	1.00
2558039--2558103	21	2.9	22	77	15	62	53	0	0	46	1.00
2562484--2562608	26	4.9	25	73	14	87	55	1	0	43	1.09
2562561--2562607	23	2.0	24	91	4	78	48	0	0	51	1.00
2562566--2562605	11	3.5	11	80	6	53	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2566478--2566577	31	3.1	31	68	21	73	43	2	1	54	1.18
2567414--2567450	18	2.1	18	90	5	58	24	0	0	75	0.80
2567413--2567457	16	2.8	15	75	18	54	28	0	0	71	0.87
2570060--2570090	4	7.8	4	100	0	62	22	0	0	77	0.77
2570455--2570519	23	2.8	23	83	6	78	40	7	12	40	1.71
2570598--2570738	54	2.8	51	74	15	139	54	4	4	36	1.42
2570803--2570869	11	6.0	11	79	8	73	50	1	1	46	1.19
2570813--2570870	23	2.6	22	89	5	82	51	1	0	46	1.11
2570803--2570872	34	2.0	35	83	8	90	50	1	1	47	1.19
2574580--2574629	23	2.1	23	85	3	64	56	0	4	40	1.18
2576685--2576737	28	2.0	27	85	7	72	62	1	0	35	1.06
2577808--2577855	25	1.9	25	86	0	69	43	2	4	50	1.33
2578003--2578071	26	2.6	26	74	23	63	46	0	2	50	1.16
2579738--2579772	2	17.5	2	100	0	70	51	0	0	48	1.00
2579772--2579802	2	15.5	2	100	0	62	51	0	48	0	1.00
2581897--2581927	2	15.5	2	93	0	53	0	0	48	51	1.00
2582924--2582962	2	19.5	2	100	0	78	51	0	0	48	1.00
2586171--2586196	1	26.0	1	100	0	52	0	0	100	0	0.00
2586532--2586589	5	11.6	5	78	14	50	46	0	0	53	1.00
2586532--2586588	22	2.3	24	80	20	64	47	0	0	52	1.00
2589418--2589442	2	12.5	2	100	0	50	52	0	0	48	1.00
2589642--2589684	21	2.0	22	86	4	61	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2591434--2591482	17	2.8	17	80	20	57	28	0	0	71	0.86
2591433--2591478	19	2.5	18	83	13	58	32	0	0	67	0.91
2592974--2593016	15	3.1	14	77	9	52	48	0	0	51	1.00
2596201--2596238	2	19.0	2	100	0	76	50	0	0	50	1.00
2596839--2596896	23	2.5	23	100	0	116	48	6	0	44	1.29
2600196--2600236	2	20.5	2	89	0	64	46	4	0	48	1.23
2604185--2604209	13	1.9	13	100	0	50	44	16	0	40	1.47
2604649--2604679	2	15.5	2	100	0	62	48	0	0	51	1.00
2606797--2606860	10	6.5	10	70	10	51	45	0	0	54	0.99
2606805--2606911	8	13.2	8	68	22	55	42	0	0	57	1.05

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