genome.fa.s3.2.7.7.80.10.50.1000.28.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  28  of  32  ( 3795 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)
4988131--4988168	15	2.7	14	80	11	51	31	7	2	57	1.41
4988666--4988706	18	2.3	18	87	8	57	31	2	0	65	1.05
4988669--4988736	22	3.4	21	70	25	58	30	1	0	67	0.99
4988662--4988719	17	3.5	17	77	13	59	32	1	0	65	1.03
4989044--4989114	28	2.7	27	73	18	69	50	0	1	47	1.09
4989103--4989145	13	3.3	12	81	15	50	53	2	2	41	1.26
4990247--4990296	19	2.7	19	76	17	52	42	2	2	54	1.23
4991800--4991854	17	3.2	18	70	12	53	34	1	0	63	1.05
4991884--4991928	14	3.2	14	80	0	54	57	0	0	42	0.98
4991884--4991939	28	2.0	27	86	3	76	60	0	0	39	0.97
4994797--4994821	2	12.5	2	100	0	50	0	0	52	48	1.00
4994819--4994852	3	11.3	3	100	0	68	0	0	67	32	0.91
4995222--4995247	3	8.7	3	100	0	52	69	0	0	30	0.89
5004763--5004789	2	13.5	2	100	0	54	48	0	0	51	1.00
5011548--5011578	2	15.5	2	100	0	62	48	0	0	51	1.00
5022581--5022623	15	2.7	16	82	7	52	58	0	0	41	0.98
5023238--5023321	33	2.5	33	84	5	107	59	0	0	40	0.97
5023244--5023321	18	4.7	16	75	22	72	57	0	0	42	0.98
5027715--5027743	6	4.8	6	100	0	58	17	17	34	31	1.93
5027887--5027925	2	20.0	2	94	5	71	51	0	0	48	1.00
5031875--5031978	29	3.7	28	68	17	72	46	2	9	41	1.51
5031870--5031986	56	2.1	55	90	3	182	44	2	9	43	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5038706--5038754	23	2.1	24	84	3	64	46	0	0	53	1.00
5038739--5038840	17	6.2	16	70	22	70	50	0	1	46	1.19
5038786--5038855	28	2.5	28	86	9	81	52	2	1	42	1.24
5041502--5041527	2	13.0	2	100	0	52	50	0	0	50	1.00
5041630--5041672	12	3.5	12	83	3	50	58	0	2	39	1.11
5041625--5041672	25	2.0	24	84	8	62	54	0	4	41	1.20
5049908--5049994	19	4.4	19	68	15	59	47	0	0	52	1.00
5050540--5050578	17	2.3	17	95	0	69	35	23	12	28	1.91
5050932--5050971	20	2.0	20	85	9	55	45	0	2	52	1.14
5051618--5051724	16	6.8	16	71	14	73	56	1	0	42	1.10
5051670--5051724	29	1.9	30	85	10	80	58	0	0	41	0.98
5061200--5061255	27	2.1	27	96	0	103	30	8	7	53	1.59
5062240--5062270	9	3.3	9	91	8	53	9	0	0	90	0.46
5062240--5062270	10	3.2	10	95	4	55	9	0	0	90	0.46
5062468--5062513	20	2.2	20	84	11	56	43	2	0	54	1.12
5065660--5065699	17	2.4	17	87	8	55	27	2	0	70	1.01
5066356--5066425	32	2.2	32	82	7	90	50	1	0	48	1.09
5076777--5076836	21	2.8	21	75	10	59	58	0	0	41	0.98
5081568--5081610	10	3.9	11	82	17	54	62	0	0	37	0.95
5081565--5081615	10	4.8	10	81	15	50	58	0	0	41	0.98
5081555--5081655	32	3.2	31	78	13	107	56	0	0	43	0.99
5081602--5081646	16	2.9	14	77	22	54	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)
5081554--5081661	33	3.3	32	79	13	114	55	0	0	44	0.99
5090301--5090346	22	2.0	23	91	4	76	65	0	0	34	0.93
5090335--5090373	18	2.1	18	85	4	51	56	2	0	41	1.13
5093345--5093371	12	2.2	12	100	0	54	92	0	7	0	0.38
5093726--5093762	3	12.3	3	94	0	65	62	0	0	37	0.96
5093893--5093975	2	42.5	2	75	13	66	43	4	1	50	1.31
5093914--5093990	23	3.0	24	82	16	93	42	6	1	49	1.36
5093900--5093977	29	2.6	30	87	6	122	43	5	1	50	1.32
5102372--5102407	2	18.0	2	100	0	72	50	0	50	0	1.00
5102637--5102821	93	2.0	93	100	0	370	33	18	14	33	1.91
5105779--5105816	17	2.2	17	86	9	51	36	0	7	55	1.29
5105847--5105890	21	2.3	18	84	11	52	63	0	2	34	1.07
5108673--5108701	2	14.5	2	100	0	58	48	0	0	51	1.00
5114825--5114857	2	16.5	2	93	0	57	48	3	0	48	1.17
5120093--5120130	20	1.9	20	84	10	51	36	2	0	60	1.11
5120235--5120291	28	2.0	29	82	6	71	57	3	0	38	1.16
5124113--5124137	2	12.5	2	100	0	50	48	0	0	52	1.00
5127866--5128099	116	2.0	116	94	0	414	38	20	12	28	1.88
5132843--5132895	24	2.2	24	83	3	63	66	7	0	26	1.18
5132949--5132983	2	17.5	2	100	0	70	48	0	0	51	1.00
5137761--5137787	2	13.5	2	100	0	54	48	0	0	51	1.00
5143635--5143659	3	8.3	3	100	0	50	68	0	0	32	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5152297--5152353	26	2.1	27	81	15	66	33	1	1	63	1.15
5154235--5154287	26	2.1	25	85	3	70	43	9	1	45	1.47
5154278--5154318	21	2.0	21	90	4	66	56	2	0	41	1.13
5155120--5155165	2	23.5	2	91	4	67	45	4	50	0	1.21
5161349--5161417	34	2.0	34	100	0	138	39	26	17	17	1.91
5164022--5164059	19	2.1	19	90	5	60	50	0	0	50	1.00
5164162--5164192	6	5.0	6	92	7	53	51	0	0	48	1.00
5164162--5164192	13	2.5	12	94	5	53	51	0	0	48	1.00
5168839--5168890	2	26.5	2	92	3	88	50	0	0	50	1.00
5173774--5173802	1	29.0	1	100	0	58	0	100	0	0	0.00
5174475--5174504	2	15.5	2	93	6	53	0	0	50	50	1.00
5175794--5175819	2	13.0	2	100	0	52	50	0	0	50	1.00
5177172--5177247	30	2.6	30	82	14	88	57	1	0	40	1.07
5178028--5178081	18	3.2	17	80	10	58	33	3	1	61	1.25
5180166--5180212	23	2.0	23	84	8	60	55	0	0	44	0.99
5180172--5180214	16	2.8	15	80	13	52	55	0	0	44	0.99
5180231--5180283	21	2.5	21	80	14	56	50	3	0	45	1.19
5182207--5182233	4	6.8	4	100	0	54	22	0	0	77	0.76
5187773--5187827	16	3.4	16	76	21	53	61	0	0	38	0.96
5193352--5193473	63	1.9	64	96	1	228	59	9	8	22	1.55
5193923--5193951	3	9.7	3	100	0	58	0	34	0	65	0.93
5195152--5195177	2	13.0	2	100	0	52	0	0	50	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5208666--5208733	32	2.1	32	100	0	136	39	16	26	17	1.90
5215226--5215252	3	9.0	3	100	0	54	33	33	0	33	1.58
5220142--5222821	537	5.0	537	97	1	5041	38	19	14	27	1.91
5225015--5225070	22	2.5	22	77	11	60	55	0	1	42	1.10
5225367--5225425	19	3.2	19	80	7	59	64	1	1	32	1.13
5227719--5228090	117	3.2	118	79	7	280	31	13	36	18	1.89
5227897--5228120	117	1.9	117	80	7	258	32	10	38	17	1.85
5235946--5235985	21	1.9	21	85	10	55	42	2	2	52	1.28
5240099--5240130	2	16.0	2	100	0	64	50	0	0	50	1.00
5240996--5241032	2	18.5	2	100	0	74	48	0	0	51	1.00
5241312--5241343	3	10.7	3	100	0	64	65	0	0	34	0.93
5244504--5244538	2	17.5	2	87	0	52	48	5	0	45	1.26
5246709--5246756	25	1.9	26	91	8	82	47	2	0	50	1.12
5248906--5248951	22	2.1	22	84	4	58	39	0	0	60	0.97
5248917--5248963	19	2.3	19	85	10	58	31	0	0	68	0.90
5248888--5248988	13	7.8	14	68	25	62	39	0	0	60	0.97
5249188--5249233	20	2.1	21	84	11	58	43	2	0	54	1.12
5249231--5249279	9	4.8	10	79	20	57	44	0	0	55	0.99
5250202--5250243	21	2.0	21	86	9	59	50	0	0	50	1.00
5250202--5250266	20	3.2	20	81	14	62	55	1	1	41	1.18
5250213--5250273	20	3.0	20	83	7	70	59	1	1	37	1.17
5250245--5250303	21	2.8	21	77	10	59	62	1	0	35	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5257164--5257198	2	17.5	2	100	0	70	51	0	48	0	1.00
5257210--5257234	13	1.9	13	100	0	50	80	0	20	0	0.72
5258051--5258087	3	12.3	3	100	0	74	32	0	0	67	0.91
5259013--5259045	16	2.1	16	94	5	59	30	3	0	66	1.06
5264021--5264054	2	17.0	2	93	0	59	50	2	0	47	1.16
5264205--5264232	2	14.0	2	100	0	56	50	0	0	50	1.00
5264984--5265034	15	3.3	15	81	8	50	54	1	1	41	1.22
5265345--5265384	20	2.0	21	90	9	66	45	0	0	55	0.99
5265419--5265479	32	1.9	32	86	6	88	40	0	0	59	0.98
5265383--5265486	16	6.5	16	70	20	67	39	0	0	59	1.04

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