genome.fa.s64.2.7.7.80.10.50.1000.27.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   34   35   36   37   38   39   40   41   42   43   44   45   

This is table  27  of  45  ( 5312 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)
4788092--4788116	11	2.3	11	100	0	50	52	0	16	32	1.44
4789669--4789707	20	2.0	20	89	0	60	33	12	15	38	1.85
4790082--4790108	14	1.9	14	100	0	54	62	0	0	37	0.95
4790369--4790399	14	2.2	14	100	0	62	58	12	6	22	1.58
4790729--4790757	13	2.1	14	93	6	51	31	3	6	58	1.41
4792546--4792594	15	3.2	16	80	11	50	69	0	0	30	0.89
4792551--4792603	24	2.3	23	83	3	61	64	0	0	35	0.94
4793031--4793082	18	3.0	18	72	16	56	38	0	0	61	0.96
4793043--4793101	13	4.5	13	71	26	52	32	0	0	67	0.91
4793046--4793101	11	5.5	11	75	16	57	32	0	0	67	0.91
4793046--4793083	16	2.4	16	91	8	60	34	0	0	65	0.93
4793978--4794020	20	2.0	22	86	8	63	60	0	2	37	1.10
4794496--4794534	20	1.9	21	94	5	71	35	23	15	25	1.94
4794544--4794581	13	2.9	13	92	0	58	31	7	15	44	1.75
4794644--4794681	20	1.9	20	88	0	58	36	10	15	36	1.82
4795128--4795211	36	2.5	35	84	7	102	32	14	22	30	1.94
4796787--4796861	21	3.5	19	75	23	53	58	2	20	18	1.51
4796908--4797112	102	2.0	102	91	0	329	44	8	13	33	1.75
4798264--4798295	11	2.9	11	90	0	55	37	0	15	46	1.46
4800025--4800069	22	2.1	21	92	8	74	46	6	8	37	1.61
4800728--4800814	36	2.6	33	81	7	86	33	14	21	29	1.94
4801228--4801264	15	2.5	14	87	12	56	75	8	0	16	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4801867--4801909	14	3.2	13	78	12	50	74	0	0	25	0.82
4801884--4801909	12	2.2	12	100	0	52	76	0	0	23	0.78
4801866--4801898	16	2.0	17	94	5	59	72	0	0	27	0.85
4801920--4801968	19	2.4	20	80	13	55	65	0	4	30	1.11
4804365--4804399	14	2.5	14	85	0	52	42	0	0	57	0.99
4804499--4804529	2	16.0	2	93	6	55	48	0	0	51	1.00
4805390--4805598	63	3.3	63	76	7	185	48	14	12	23	1.78
4806389--4806428	21	1.9	21	94	0	71	42	32	5	20	1.73
4806566--4806655	22	4.2	22	81	2	85	46	8	6	37	1.61
4807229--4807293	30	2.2	30	88	0	94	50	13	4	30	1.62
4807515--4807567	2	25.5	2	78	14	54	47	3	3	45	1.39
4807491--4807567	36	2.2	36	90	2	120	45	5	5	44	1.48
4808061--4808118	20	2.9	20	84	5	73	31	17	13	37	1.89
4808064--4808401	164	2.1	164	93	1	579	29	17	13	39	1.88
4811644--4811702	22	2.7	22	89	0	82	44	6	5	44	1.52
4811655--4811725	22	3.1	22	85	4	70	49	2	2	45	1.31
4811907--4811981	22	3.4	22	78	14	82	45	13	5	36	1.66
4812517--4812615	30	3.3	29	78	2	81	51	10	5	33	1.57
4812539--4812649	29	3.8	30	82	4	120	51	8	5	35	1.55
4812597--4812650	16	3.6	15	80	16	67	55	0	3	40	1.17
4812900--4812957	8	7.0	8	83	13	55	31	0	0	68	0.89
4812917--4812958	8	4.8	9	91	8	61	30	0	0	69	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4819657--4819722	26	2.4	27	83	14	75	46	6	3	43	1.43
4822689--4822772	25	3.3	24	75	21	73	39	0	2	58	1.11
4822688--4822763	29	2.7	29	82	13	88	40	0	2	56	1.13
4826434--4826475	17	2.5	17	80	3	50	69	2	2	26	1.13
4826444--4826485	22	1.9	22	85	9	59	73	2	0	23	0.94
4826687--4826842	83	1.9	84	82	5	199	32	5	14	47	1.66
4827216--4827255	2	20.0	2	100	0	80	50	0	0	50	1.00
4832266--4832390	52	2.4	52	97	0	232	27	17	19	36	1.94
4837159--4837210	22	2.3	23	81	18	58	57	0	1	40	1.10
4837526--4837625	29	3.2	29	80	14	119	54	4	9	33	1.51
4838380--4838441	22	2.9	21	79	9	72	45	8	1	45	1.42
4840590--4840668	22	3.9	21	67	23	60	41	0	0	58	0.98
4841749--4841788	2	20.0	2	100	0	80	50	0	0	50	1.00
4841963--4842001	19	2.0	20	85	14	55	61	2	0	35	1.10
4843771--4843814	3	14.7	3	100	0	88	0	31	0	68	0.90
4849439--4849626	94	2.0	94	98	0	367	39	16	10	33	1.83
4858081--4858250	85	2.0	84	95	1	304	33	13	15	37	1.87
4858974--4859086	56	2.0	56	100	0	226	31	12	17	38	1.87
4860028--4860059	2	16.0	2	100	0	64	50	0	0	50	1.00
4862903--4862959	29	2.0	29	86	6	80	31	12	17	38	1.87
4873398--4873432	13	2.7	13	86	0	52	22	0	0	77	0.78
4873386--4873436	23	2.2	23	89	0	75	21	1	0	76	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4873380--4873468	34	2.5	37	74	18	91	24	2	0	73	0.95
4873380--4873464	23	3.7	22	77	12	73	24	1	0	74	0.89
4873398--4873465	26	2.6	25	84	9	75	23	0	0	76	0.79
4873954--4873978	2	12.5	2	100	0	50	52	0	0	48	1.00
4874985--4875014	2	15.0	2	92	0	51	3	50	0	46	1.18
4878347--4878485	69	2.0	68	97	1	260	32	7	22	38	1.81
4882897--4882927	3	10.3	3	100	0	62	35	0	0	64	0.94
4884061--4884092	14	2.3	15	89	10	50	0	0	6	93	0.34
4884061--4884091	9	3.6	9	95	4	55	0	0	6	93	0.35
4884995--4885063	13	5.2	13	75	18	54	40	0	1	57	1.07
4885016--4885076	19	3.2	18	77	20	54	45	0	0	54	1.00
4887482--4887538	23	2.4	25	77	19	68	56	0	1	42	1.10
4887876--4887919	16	2.8	16	82	3	54	84	0	9	6	0.79
4892136--4892215	30	2.6	31	86	5	119	31	15	11	42	1.81
4897001--4897038	2	19.5	2	94	5	69	50	0	0	50	1.00
4898359--4898395	2	18.5	2	100	0	74	48	0	51	0	1.00
4904379--4904432	17	3.2	16	79	7	63	37	0	0	62	0.95
4905851--4905905	28	1.9	27	82	10	65	49	3	1	45	1.30
4907350--4907411	26	2.3	26	83	5	79	54	1	1	41	1.19
4907367--4907442	34	2.3	34	84	13	104	55	0	0	44	0.99
4916301--4916476	90	2.0	90	87	0	253	33	14	17	35	1.89
4918444--4918498	25	2.2	25	93	0	92	5	32	10	50	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4920036--4920091	28	2.0	28	92	0	94	25	16	16	42	1.87
4922610--4922655	17	2.6	18	80	19	53	32	13	6	47	1.68
4931385--4931416	2	16.0	2	100	0	64	50	0	0	50	1.00
4931502--4931575	32	2.3	32	100	0	148	33	5	10	50	1.60
4931602--4931844	31	8.2	30	74	16	186	56	5	8	28	1.52
4931602--4931811	15	13.3	15	66	21	92	57	5	9	27	1.52
4931619--4931846	62	3.9	59	79	13	265	57	5	8	28	1.51
4931703--4931752	22	2.3	22	86	3	66	60	2	8	30	1.37
4931671--4931864	53	3.5	54	77	15	198	58	5	8	27	1.51
4931614--4931865	114	2.2	114	91	2	402	57	5	8	28	1.50
4931602--4931844	15	15.4	14	66	20	67	56	5	8	28	1.52
4932494--4932556	3	21.0	3	100	0	126	66	0	0	33	0.92
4934879--4935259	29	14.0	29	64	14	148	21	35	15	27	1.94
4934873--4935549	81	8.4	81	91	1	1051	22	33	16	27	1.95
4934873--4935627	239	3.1	238	85	4	903	22	33	16	27	1.95
4935572--4935622	26	2.0	26	84	7	68	23	39	15	21	1.92
4938125--4938159	16	2.2	16	90	10	54	45	8	0	45	1.34
4938710--4938750	22	1.9	21	85	5	55	56	0	4	39	1.21
4939825--4939851	14	1.9	14	100	0	54	55	7	0	37	1.28
4940124--4940224	43	2.3	43	98	0	193	68	4	14	11	1.36
4943041--4943084	21	2.1	21	100	0	88	45	0	27	27	1.54
4943843--4943879	17	2.3	15	90	9	56	8	0	2	89	0.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4943844--4943868	10	2.5	10	100	0	50	8	0	0	92	0.40
4945154--4945179	2	13.0	2	100	0	52	50	0	0	50	1.00
4945829--4945886	26	2.3	26	82	11	75	5	18	0	75	0.98
4945921--4945965	2	22.5	2	95	0	81	46	0	53	0	1.00
4946342--4946384	18	2.3	19	84	4	52	60	0	0	39	0.97
4947307--4947336	2	15.0	2	92	0	51	46	0	3	50	1.18
4949964--4949999	6	6.0	6	96	0	63	33	16	13	36	1.89
4951900--4952104	105	2.0	105	97	0	383	29	17	17	36	1.93
4957010--4957037	13	2.2	13	100	0	56	28	14	17	39	1.89
4956992--4957056	33	2.0	33	87	6	96	30	15	12	41	1.84

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   34   35   36   37   38   39   40   41   42   43   44   45