genome.fa.s4.2.7.7.80.10.50.1000.26.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  26  of  31  ( 3628 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)
5217836--5218068	50	4.6	50	93	0	385	30	20	20	28	1.98
5220463--5220507	22	2.0	24	86	8	67	35	6	0	57	1.25
5221811--5222579	297	2.6	294	86	4	1003	41	11	9	37	1.74
5222682--5222710	2	14.5	2	100	0	58	48	0	0	51	1.00
5223004--5223048	20	2.2	20	96	0	81	62	4	15	17	1.49
5223786--5223815	13	2.2	13	94	5	51	63	0	0	36	0.95
5223795--5223835	20	2.1	19	86	4	55	60	2	0	36	1.10
5225451--5225492	12	3.8	11	78	9	50	23	2	2	71	1.10
5236993--5237213	34	6.5	33	80	9	248	41	25	7	25	1.82
5236993--5237213	102	2.2	101	89	1	352	41	25	7	25	1.82
5241622--5241842	34	6.5	33	80	9	248	41	26	7	24	1.82
5241624--5241842	68	3.2	67	83	3	278	41	26	7	25	1.82
5241622--5241842	102	2.2	101	89	1	352	41	26	7	24	1.82
5246250--5246328	34	2.3	33	83	10	106	39	29	7	24	1.82
5246151--5246503	175	2.0	175	99	0	697	35	21	12	30	1.90
5246425--5246643	34	6.5	33	80	9	244	41	26	7	25	1.81
5246427--5246643	68	3.2	67	84	3	274	41	26	7	25	1.81
5246425--5246643	102	2.2	101	89	1	348	41	26	7	25	1.81
5248370--5248447	36	2.2	36	90	4	122	23	29	7	39	1.82
5249425--5249475	14	3.6	14	76	10	50	49	0	0	50	1.00
5249462--5249503	14	2.9	14	82	3	57	54	2	2	40	1.26
5249461--5249612	12	12.2	12	68	22	57	48	2	2	46	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5255405--5255529	52	2.4	52	94	0	214	28	17	17	36	1.93
5255405--5255549	52	2.8	51	88	4	202	30	17	17	34	1.93
5255538--5255562	13	1.9	13	100	0	50	36	16	16	32	1.90
5255625--5255649	13	1.9	13	100	0	50	32	16	16	36	1.90
5255604--5255669	33	2.0	33	91	2	107	37	15	10	36	1.82
5261067--5261121	24	2.3	24	87	12	78	49	1	0	49	1.11
5262787--5262838	15	3.6	14	76	19	61	53	1	0	44	1.11
5262847--5262871	13	1.9	13	100	0	50	56	0	4	40	1.18
5265293--5265340	21	2.3	21	100	0	96	16	35	4	43	1.67
5269518--5269543	3	8.7	3	100	0	52	34	0	0	65	0.93
5270966--5271017	20	2.6	19	81	6	59	34	3	1	59	1.27
5271420--5271457	10	3.8	10	89	10	60	68	0	0	31	0.90
5271421--5271462	19	2.1	21	91	8	70	64	0	0	35	0.94
5272285--5272319	15	2.2	16	90	5	54	51	0	0	48	1.00
5273008--5273042	11	3.3	11	88	8	54	31	0	0	68	0.90
5273037--5273075	20	2.0	20	85	10	53	46	0	2	51	1.14
5273057--5273135	29	2.8	27	76	12	79	39	1	1	58	1.14
5273689--5273718	15	2.0	15	93	0	51	23	0	0	76	0.78
5273951--5273984	15	2.4	14	85	9	50	50	2	5	41	1.42
5275795--5275828	17	2.1	16	88	5	50	58	0	0	41	0.98
5277351--5277409	24	2.3	25	82	11	75	61	0	0	38	0.96
5277861--5277962	35	3.1	35	72	18	103	48	0	0	50	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5278212--5278281	17	4.2	16	75	18	63	47	0	0	52	1.00
5278210--5278269	26	2.4	25	82	2	75	48	0	0	51	1.00
5278226--5278287	17	3.8	17	81	12	67	45	0	0	54	0.99
5278402--5278426	11	2.3	11	100	0	50	92	0	8	0	0.40
5289103--5289149	3	15.7	3	95	0	85	31	2	0	65	1.04
5295273--5295323	23	2.2	22	86	10	75	25	3	19	50	1.64
5295281--5295344	23	2.8	23	90	2	94	26	3	21	48	1.65
5298098--5298172	20	3.8	19	77	7	78	26	16	14	42	1.86
5300472--5300615	51	2.8	51	84	0	198	31	23	11	34	1.90
5300602--5300675	28	2.6	29	83	10	91	20	29	21	28	1.98
5300716--5300784	28	2.5	27	83	9	86	26	31	13	28	1.93
5300590--5300828	109	2.2	109	80	5	274	27	24	14	33	1.94
5303015--5303046	9	3.8	9	88	12	50	0	0	9	90	0.45
5312087--5312142	28	2.1	26	87	12	78	51	0	0	48	1.00
5312097--5312145	25	2.0	25	87	0	71	46	0	0	53	1.00
5312123--5312177	16	3.2	17	75	25	62	36	3	0	60	1.15
5312678--5312721	22	2.0	22	86	8	63	54	0	0	45	0.99
5312651--5312717	28	2.3	31	79	12	86	49	0	0	50	1.00
5313288--5313312	2	12.5	2	100	0	50	52	0	0	48	1.00
5313673--5313737	33	2.0	33	81	0	76	46	6	4	43	1.49
5313782--5313825	23	2.0	22	83	16	56	36	0	2	61	1.09
5315151--5315188	2	19.5	2	86	5	51	55	0	2	42	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5316378--5316418	20	2.0	21	90	4	66	53	0	0	46	1.00
5318372--5318412	3	13.3	3	94	5	73	65	0	0	34	0.93
5318761--5318883	47	2.6	48	79	11	144	39	18	2	39	1.64
5320999--5321045	19	2.5	20	82	10	62	31	2	2	63	1.18
5323135--5323173	20	2.0	20	89	0	60	35	10	5	48	1.59
5323311--5323366	28	2.1	26	87	12	78	51	0	0	48	1.00
5323321--5323369	25	2.0	25	87	0	71	46	0	0	53	1.00
5323710--5323743	15	2.3	15	89	0	50	50	0	0	50	1.00
5323887--5323953	29	2.3	29	78	17	75	47	0	1	50	1.10
5324003--5324041	19	2.0	20	90	5	62	51	5	0	43	1.24
5324534--5324570	2	18.5	2	100	0	74	51	0	0	48	1.00
5325001--5325044	14	3.3	13	81	12	54	52	0	2	45	1.13
5326682--5326717	2	18.0	2	100	0	72	50	0	0	50	1.00
5328866--5328900	6	5.8	6	93	0	61	51	2	31	14	1.57
5329414--5329451	19	2.0	20	89	5	60	36	0	0	63	0.95
5330024--5330054	16	1.9	16	93	0	53	54	3	16	25	1.56
5331323--5331379	19	3.1	19	74	25	59	57	0	0	42	0.98
5331622--5331670	20	2.6	18	78	12	53	44	0	0	55	0.99
5332558--5332583	3	8.7	3	100	0	52	30	0	0	69	0.89
5336679--5336709	2	15.5	2	93	0	53	0	45	3	51	1.17
5341501--5341526	2	13.0	2	100	0	52	50	0	0	50	1.00
5343899--5343941	22	2.0	21	86	9	59	48	4	2	44	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5344741--5344774	14	2.4	14	90	0	50	61	0	2	35	1.11
5345185--5345220	18	2.0	18	89	10	56	47	0	0	52	1.00
5345178--5345239	33	1.9	31	81	12	72	50	0	1	48	1.10
5347116--5347162	15	3.1	15	81	12	51	55	0	0	44	0.99
5347127--5347169	8	5.5	8	83	10	54	51	0	2	46	1.13
5347634--5347668	16	2.2	16	94	0	61	45	2	0	51	1.16
5349096--5349120	2	12.5	2	100	0	50	48	0	0	52	1.00
5349670--5349709	20	2.0	21	85	5	55	35	2	0	62	1.09
5350549--5350587	17	2.3	16	86	8	51	82	7	2	7	0.94
5351389--5351422	14	2.4	14	90	0	50	61	0	0	38	0.96
5351688--5351733	21	2.1	23	84	15	62	50	2	0	47	1.13
5351937--5351975	18	2.1	19	90	4	62	66	0	2	30	1.05
5361535--5361574	2	20.5	2	94	5	73	50	0	0	50	1.00
5362592--5362654	32	2.0	32	90	6	101	36	1	0	61	1.05
5362594--5362651	19	2.8	20	74	18	57	32	1	0	65	1.03
5364274--5364314	20	2.0	21	90	9	66	60	0	0	39	0.96
5368028--5368072	3	15.0	3	95	0	81	66	0	2	31	1.04
5368308--5368335	2	14.0	2	100	0	56	50	0	0	50	1.00
5369345--5369385	21	2.0	21	100	0	82	34	14	21	29	1.93
5371682--5371739	28	2.1	28	90	0	89	43	5	13	37	1.67
5372354--5372402	20	2.4	20	90	10	73	40	2	2	55	1.23
5372905--5372978	31	2.4	32	84	11	84	45	0	12	41	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5374182--5374227	23	2.0	23	87	8	67	50	0	0	50	1.00
5376311--5376342	2	16.0	2	100	0	64	0	50	0	50	1.00
5376342--5376371	2	15.0	2	100	0	60	50	0	0	50	1.00
5377100--5377145	21	2.2	21	88	7	67	52	0	4	43	1.21
5382926--5383057	54	2.4	53	91	5	219	21	11	26	40	1.87
5389826--5389928	52	2.0	52	100	0	206	30	7	13	48	1.71
5394970--5395095	65	1.9	65	80	6	148	53	0	1	43	1.15
5395016--5395122	49	2.3	45	80	13	117	58	0	0	41	0.98
5396731--5396757	14	1.9	14	100	0	54	33	0	0	66	0.92
5396973--5397044	30	2.5	28	76	10	74	41	1	1	55	1.17

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