genome.fa.s35.2.7.7.80.10.50.1000.29.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: Scaffold35
Parameters: 2 7 7 80 10 50 1000
Length:  4812169

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   

This is table  29  of  30  ( 3549 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)
4557232--4557292	30	2.0	30	90	6	97	34	16	14	34	1.89
4562108--4562397	162	1.8	160	85	3	411	43	12	10	33	1.77
4563872--4564608	165	4.5	166	82	5	816	52	8	10	28	1.65
4563875--4564608	327	2.2	329	84	4	937	52	8	9	28	1.64
4565533--4565617	27	3.1	27	79	3	73	23	24	11	40	1.88
4565415--4565648	34	7.3	33	76	12	145	21	23	11	44	1.84
4565586--4565655	33	2.1	33	84	5	88	17	25	11	45	1.81
4565649--4566018	31	11.7	33	78	10	292	32	31	16	19	1.94
4565664--4566058	63	6.2	63	80	5	359	32	30	17	19	1.95
4565687--4566058	32	11.7	31	78	5	273	32	30	17	19	1.95
4566136--4566424	52	5.4	52	75	11	199	24	25	14	35	1.94
4566274--4566584	61	5.2	61	74	9	268	24	27	12	35	1.91
4566222--4566503	113	2.5	113	82	1	332	25	26	12	35	1.92
4567141--4567194	20	2.7	20	91	8	83	38	12	18	29	1.88
4567141--4567214	21	3.6	21	83	7	71	36	14	20	28	1.92
4567237--4567314	40	2.0	40	86	0	111	33	10	12	43	1.77
4574502--4574544	2	21.5	2	100	0	86	51	0	0	48	1.00
4577119--4577164	22	2.1	21	84	4	56	28	2	2	67	1.14
4577255--4577596	125	2.7	126	93	0	596	45	11	7	35	1.67
4578020--4578068	12	3.8	12	75	19	53	26	0	2	71	0.97
4579291--4579677	120	3.4	111	80	12	450	51	2	2	43	1.29
4579562--4579652	33	2.7	34	83	10	114	48	0	1	50	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4579562--4579652	34	2.7	35	80	14	100	48	0	1	50	1.08
4579906--4579935	15	2.0	15	93	0	51	36	0	0	63	0.95
4579952--4580001	25	2.1	24	85	10	68	36	0	0	64	0.94
4581894--4582235	156	2.2	155	84	3	443	42	18	14	25	1.87
4583976--4584098	58	2.1	58	89	0	192	1	17	21	58	1.47
4584443--4584476	17	2.0	17	88	11	52	5	26	14	52	1.64
4584905--4584940	18	2.0	17	89	10	54	77	2	2	16	1.00
4590591--4590615	13	1.9	13	100	0	50	36	16	16	32	1.90
4590571--4590637	33	2.0	33	88	0	98	32	11	14	40	1.83
4590678--4590702	13	1.9	13	100	0	50	32	16	16	36	1.90
4590711--4590839	52	2.5	52	94	0	222	33	19	17	29	1.95
4595309--4595333	13	1.9	13	100	0	50	36	16	16	32	1.90
4595322--4595370	19	2.6	19	87	3	55	34	10	14	40	1.79
4595422--4595446	13	1.9	13	100	0	50	32	16	16	36	1.90
4597630--4597683	27	2.1	26	86	10	76	24	38	16	20	1.92
4598707--4598774	34	2.0	34	94	0	118	33	17	26	22	1.96
4602510--4602552	18	2.4	18	84	7	52	65	16	9	9	1.47
4602639--4602694	19	2.9	18	79	12	58	69	1	25	3	1.14
4602645--4602694	17	3.0	16	78	18	57	68	2	28	2	1.12
4602705--4602751	24	2.0	24	91	0	76	68	12	12	6	1.39
4602815--4602849	16	2.2	16	90	10	54	54	25	14	5	1.62
4602872--4602919	25	1.9	25	82	0	60	47	20	16	14	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4609199--4609223	13	1.9	13	100	0	50	36	16	16	32	1.90
4617174--4617212	2	19.5	2	100	0	78	51	0	0	48	1.00
4617245--4617270	7	3.7	7	100	0	52	76	11	0	11	1.01
4617536--4617591	18	3.1	18	71	19	53	17	5	10	66	1.41
4617517--4617603	36	2.4	36	79	9	95	21	3	6	67	1.29
4619438--4619522	44	1.9	44	97	0	161	47	12	12	27	1.79
4619804--4620003	58	3.5	56	76	10	163	49	12	10	28	1.73
4619872--4620172	58	5.2	57	73	13	206	48	15	9	26	1.75
4619920--4620127	115	1.8	115	79	9	244	47	16	9	26	1.77
4620162--4620313	58	2.6	58	79	5	148	48	15	7	27	1.73
4622627--4622677	20	2.6	19	87	12	68	35	17	11	35	1.87
4623642--4623763	62	2.0	62	86	3	174	45	9	10	33	1.72
4623947--4624014	35	2.0	35	83	13	88	44	7	0	48	1.30
4624613--4624647	6	6.0	6	93	6	63	48	51	0	0	1.00
4624613--4624647	11	3.0	12	91	8	63	48	51	0	0	1.00
4627000--4627026	2	13.5	2	100	0	54	48	0	0	51	1.00
4629316--4629430	32	3.6	32	72	4	97	32	12	19	36	1.88
4639568--4639607	16	2.4	17	87	4	55	52	12	15	20	1.74
4639612--4639655	19	2.4	19	88	3	63	45	18	15	20	1.85
4643669--4643764	31	3.1	31	90	0	165	39	23	6	30	1.79
4645647--4645819	84	2.1	84	95	0	310	28	5	34	31	1.81
4648014--4648109	31	3.1	31	87	1	147	39	22	6	31	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4649340--4649432	27	3.3	27	63	14	69	38	10	22	27	1.87
4649329--4649459	59	2.2	59	98	0	253	41	11	22	24	1.86
4650028--4650064	2	18.5	2	100	0	74	48	0	0	51	1.00
4650849--4650892	16	2.8	16	85	0	61	2	4	43	50	1.35
4650868--4650952	16	5.4	16	80	2	91	7	15	37	40	1.74
4650852--4650951	32	3.2	32	81	4	96	7	13	38	42	1.71
4650892--4650952	31	1.9	32	86	3	88	9	19	32	37	1.85
4652530--4652583	16	3.4	16	92	0	90	5	12	33	48	1.65
4652816--4652848	12	2.8	12	95	0	57	24	15	30	30	1.95
4652767--4652888	61	2.0	61	93	0	208	34	11	22	31	1.90
4659463--4659508	24	2.0	22	83	8	56	63	2	2	32	1.19
4659761--4659838	21	3.6	21	68	10	57	38	2	0	58	1.12
4664329--4664373	22	2.0	22	86	4	63	48	2	0	48	1.13
4664673--4664710	15	2.7	14	84	11	51	47	0	7	44	1.32
4664604--4664750	70	2.1	70	81	6	163	48	2	5	43	1.40
4665656--4665687	3	10.7	3	100	0	64	31	0	0	68	0.90
4666386--4666414	13	2.2	13	100	0	58	48	0	6	44	1.29
4673950--4674030	36	2.3	35	81	10	85	71	9	13	4	1.28
4674283--4674316	1	34.0	1	93	0	50	94	5	0	0	0.32
4674283--4674318	18	2.0	18	100	0	72	88	11	0	0	0.50
4675369--4676545	27	43.0	27	91	2	1850	22	34	14	28	1.93
4676528--4677001	32	14.8	32	93	1	745	31	33	18	16	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4678264--4678309	23	2.0	24	86	4	67	76	0	17	6	1.00
4681048--4681264	34	6.4	34	85	2	276	25	7	26	40	1.82
4681048--4681264	102	2.1	101	91	1	353	25	7	26	40	1.82
4685675--4685893	34	6.5	34	85	2	280	25	7	26	40	1.82
4685675--4685893	102	2.2	101	91	1	357	25	7	26	40	1.82
4686274--4686299	3	8.7	3	100	0	52	30	0	0	69	0.89
4689133--4689177	25	1.9	23	86	13	65	71	2	11	15	1.24
4691680--4691711	3	10.7	3	100	0	64	68	0	0	31	0.90
4691710--4691747	3	12.7	3	100	0	76	68	0	31	0	0.90
4694539--4694603	16	4.1	16	72	7	51	46	10	10	32	1.73
4694546--4694630	32	2.7	32	74	7	91	50	7	10	31	1.64
4698792--4698839	21	2.3	21	88	0	69	29	22	8	39	1.83
4703839--4703909	35	2.0	35	97	0	133	22	9	11	56	1.64
4705974--4706021	13	3.7	13	75	8	53	60	6	6	27	1.45
4709033--4709084	28	1.9	27	88	7	79	32	21	26	19	1.97
4709070--4709185	51	2.3	51	87	0	169	29	11	27	31	1.91
4708913--4709135	78	2.8	79	75	11	215	35	13	22	29	1.92
4709168--4709243	28	2.8	28	88	6	111	25	19	32	22	1.97
4709281--4709348	28	2.4	27	88	9	93	26	17	30	25	1.97
4709341--4709480	51	2.7	51	76	6	149	35	10	22	32	1.87
4711801--4711874	20	3.7	19	87	7	103	41	13	16	28	1.86
4711893--4711943	20	2.5	20	87	6	68	41	11	15	31	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4712554--4712596	15	2.9	15	79	6	52	55	2	18	23	1.54
4712642--4712671	4	7.8	4	92	7	53	76	0	0	23	0.78
4713435--4713493	29	2.0	28	81	12	66	40	0	1	57	1.09
4713452--4713503	14	3.6	14	84	5	68	40	0	0	59	0.97
4713456--4713496	21	2.0	21	86	13	59	39	0	0	60	0.96
4713454--4713512	22	2.7	22	80	15	61	42	0	0	57	0.98
4713443--4713513	29	2.4	30	81	11	83	46	0	0	53	1.00
4713502--4713544	17	2.6	18	85	10	56	67	0	0	32	0.91
4713624--4713670	21	2.1	23	88	7	71	40	0	0	59	0.97
4713730--4713780	15	3.5	14	75	17	50	64	1	0	33	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