genome.fa.s49.2.7.7.80.10.50.1000.3.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: Scaffold49
Parameters: 2 7 7 80 10 50 1000
Length:  1668912

Tables:   1   2   3   4   5   6   7   8   9   

This is table  3  of  9  ( 1071 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)
331177--331231	21	2.7	21	80	5	69	34	12	14	38	1.84
333664--333797	52	2.6	51	82	3	169	32	25	9	32	1.88
333810--334044	79	3.0	78	77	5	238	26	26	14	32	1.95
342636--342694	28	2.1	28	81	3	66	69	6	0	23	1.12
343007--343058	24	2.2	24	89	3	79	57	0	38	3	1.17
343261--343290	8	3.9	8	95	4	53	46	0	0	53	1.00
343268--343368	20	5.4	19	71	17	70	39	0	0	58	1.11
343293--343370	19	4.1	18	72	19	61	37	1	1	60	1.13
343469--343578	10	10.9	10	69	19	52	57	1	1	39	1.20
343540--343594	23	2.4	22	80	17	58	61	0	0	38	0.96
343512--343592	41	1.9	41	82	9	101	60	0	0	39	0.97
343630--343663	13	2.5	14	85	9	52	76	0	0	23	0.79
343697--343736	20	2.0	20	90	4	64	40	0	0	60	0.97
343896--343944	25	2.0	25	84	8	64	53	0	0	46	1.00
347869--347894	2	13.0	2	100	0	52	0	50	0	50	1.00
352761--352812	27	2.0	25	85	11	68	46	7	1	44	1.43
352826--352861	18	2.0	18	94	0	63	63	0	0	36	0.94
357833--357872	15	2.7	15	96	0	71	30	12	20	37	1.89
361737--361805	32	2.2	32	89	0	102	36	13	15	34	1.87
361822--361862	21	2.0	21	90	0	64	41	7	19	31	1.79
364229--364350	52	2.4	51	86	6	167	32	24	11	31	1.91
364334--364408	27	2.7	28	85	6	100	25	32	18	24	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
364361--364534	79	2.2	79	81	9	187	27	26	14	32	1.95
364472--364634	51	3.2	51	80	4	161	27	26	12	32	1.93
364694--364746	27	2.0	27	92	0	88	24	30	18	26	1.98
364754--364974	51	4.3	51	82	2	237	30	25	11	32	1.91
364805--364974	52	3.3	51	85	4	225	31	26	11	31	1.91
364957--365038	28	2.9	29	78	8	89	25	30	17	26	1.97
371347--371475	52	2.5	52	96	0	240	27	19	17	34	1.95
371463--371488	13	2.0	13	100	0	52	38	15	15	30	1.88
371533--371681	32	4.7	32	94	1	255	36	17	12	32	1.88
371576--371667	19	5.5	19	67	28	82	39	19	11	29	1.88
373807--373927	50	2.4	51	87	2	172	41	10	20	27	1.85
375092--375168	31	2.5	32	80	6	86	53	12	9	24	1.68
375101--375168	16	4.4	16	69	12	52	55	13	10	20	1.66
378285--378325	21	2.0	21	85	9	57	46	14	19	19	1.84
379327--379375	20	2.4	21	86	3	64	34	16	10	38	1.82
379788--379828	15	2.9	15	82	7	50	78	4	0	17	0.93
379966--380092	63	2.0	63	92	0	209	33	9	4	51	1.55
380265--380297	15	2.2	15	89	10	50	51	3	3	42	1.32
380271--380309	21	1.9	21	89	5	62	56	5	0	38	1.22
382281--382340	31	1.9	31	96	0	111	33	11	13	41	1.80
390217--390297	29	2.9	28	80	8	94	50	0	1	48	1.08
390740--391349	203	3.0	203	94	0	1067	22	13	17	46	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
391576--391614	2	19.5	2	100	0	78	0	48	0	51	1.00
398575--398605	2	15.5	2	100	0	62	48	0	0	51	1.00
405750--405799	6	8.3	6	90	0	82	50	2	36	12	1.51
406940--406974	10	3.4	10	92	4	52	34	0	2	62	1.10
409667--409697	12	2.6	12	89	0	53	0	9	0	90	0.46
413111--413167	16	3.6	16	75	0	51	10	19	26	43	1.83
413313--413345	15	2.2	16	89	10	52	36	0	0	63	0.95
413330--413367	20	1.9	19	89	5	58	44	2	0	52	1.14
414372--414400	4	7.2	4	100	0	58	24	0	0	75	0.80
415967--416022	29	1.9	29	92	0	94	39	17	10	32	1.84
417125--417167	21	2.0	22	95	4	79	37	4	9	48	1.56
418632--418738	17	6.3	16	72	12	63	42	1	0	55	1.17
418650--418693	11	3.8	12	83	16	58	34	0	0	65	0.93
418630--418694	28	2.3	27	76	7	67	38	1	0	60	1.07
418742--418790	21	2.3	22	85	3	64	71	4	0	24	1.03
419178--419207	14	2.1	14	93	0	51	53	0	0	46	1.00
419181--419253	31	2.4	29	82	11	85	50	0	0	49	1.00
420521--420570	22	2.3	23	83	12	63	60	0	0	40	0.97
421065--421147	29	2.8	29	76	20	84	37	0	0	62	0.95
421070--421141	30	2.3	32	83	9	105	40	0	0	59	0.97
421187--421232	21	2.1	22	84	4	58	41	8	4	45	1.55
421187--421239	21	2.4	21	81	6	52	39	11	3	45	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
421270--421335	20	3.3	21	79	10	77	36	1	1	60	1.15
422503--422583	10	7.5	11	73	19	55	55	1	0	43	1.07
422573--422604	16	1.9	17	93	6	57	68	3	0	28	1.04
423102--423138	17	2.2	17	90	0	56	70	2	2	24	1.14
423546--423585	10	3.6	11	83	10	55	57	0	0	42	0.98
423544--423585	11	3.8	11	84	9	59	59	0	0	40	0.97
423544--423584	21	1.9	22	95	5	75	60	0	0	39	0.96
423693--423762	18	3.3	20	80	17	72	45	0	0	54	0.99
427937--428011	22	3.3	22	70	12	71	62	0	6	30	1.21
427939--428036	46	2.1	47	98	1	189	59	0	10	30	1.31
428550--428594	21	2.1	21	84	8	56	28	17	8	44	1.79
430008--430032	12	2.1	12	100	0	50	40	8	8	44	1.63
432930--433212	155	1.8	154	81	6	331	39	20	17	22	1.92
435300--435681	166	2.3	164	82	7	452	50	8	11	30	1.68
435300--435786	166	2.9	164	79	8	429	50	7	10	31	1.64
441449--442295	155	5.5	156	75	11	556	37	18	19	25	1.93
441709--442292	158	3.7	154	76	13	499	37	17	19	25	1.93
444011--444064	23	2.4	22	81	9	56	12	18	29	38	1.88
444296--444346	28	1.9	25	95	0	66	0	25	11	62	1.29
444783--444816	15	2.4	14	90	5	50	70	2	2	23	1.15
445003--445360	165	2.2	166	82	6	415	49	7	11	32	1.66
445059--445360	166	1.8	165	84	5	412	49	7	11	31	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
446886--447031	77	1.9	77	100	0	292	34	12	15	38	1.84
449705--449736	2	16.0	2	100	0	64	50	0	0	50	1.00
455396--455445	20	2.5	20	83	3	64	34	18	8	40	1.79
457431--457482	25	2.0	26	85	3	70	50	0	0	50	1.00
457793--457894	32	3.1	32	72	13	89	40	0	0	59	0.97
457781--457899	34	3.5	34	72	22	106	37	0	0	60	1.09
457824--457898	30	2.6	29	79	10	82	38	0	0	61	0.96
457819--457973	59	2.5	61	80	10	181	41	1	0	56	1.12
457969--458028	21	3.0	19	70	18	50	46	5	0	48	1.24
458238--458284	16	2.9	16	78	9	51	57	10	0	31	1.33
458250--458297	16	2.9	16	84	6	51	58	10	0	31	1.32
458370--458460	40	2.3	39	88	7	130	47	8	12	31	1.71
458392--458456	19	3.4	19	71	10	60	44	7	12	35	1.71
459998--460023	2	13.0	2	100	0	52	50	0	50	0	1.00
460412--460449	20	1.9	19	89	5	58	71	0	0	28	0.87
460413--460457	14	3.3	14	81	6	56	71	0	0	28	0.87
460415--460457	13	3.2	13	81	15	52	72	0	0	27	0.85
466500--466525	13	2.0	13	100	0	52	38	15	15	30	1.88
466482--466546	32	2.0	32	87	6	94	43	15	13	27	1.85
467659--467708	21	2.3	21	80	10	57	56	4	18	22	1.58
471557--471594	13	2.9	13	92	0	58	36	18	13	31	1.89
471706--471751	21	2.2	20	81	11	58	32	19	4	43	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
473432--473522	39	2.3	40	79	9	105	37	5	23	34	1.78
474167--474192	13	2.0	13	100	0	52	38	15	15	30	1.88
474149--474213	32	2.0	32	87	6	94	43	15	13	27	1.85
475092--475149	29	1.9	31	86	6	84	50	1	1	46	1.22
475302--475338	15	2.6	14	87	8	56	54	2	0	43	1.14
475354--475395	22	1.9	22	85	0	57	42	0	2	54	1.13
475365--475470	39	2.8	37	71	22	94	46	1	1	50	1.23
475444--475477	17	1.9	17	88	5	50	55	0	0	44	0.99
475517--475562	14	3.3	14	80	17	51	45	2	0	52	1.13
475498--475562	29	2.2	29	81	5	69	43	1	4	50	1.32

Tables:   1   2   3   4   5   6   7   8   9