genome.fa.s4.2.7.7.80.10.50.1000.24.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  24  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)
4936071--4936102	3	10.7	3	100	0	64	65	0	0	34	0.93
4937027--4937074	2	23.0	2	87	8	69	45	4	2	47	1.33
4937281--4937488	11	17.9	12	68	21	108	62	0	1	35	1.11
4937310--4937399	21	4.1	21	77	11	92	66	0	1	32	0.99
4937312--4937373	12	5.1	12	77	14	56	70	0	0	29	0.87
4937339--4937392	15	3.4	16	72	25	51	66	0	1	31	1.02
4937361--4937421	25	2.4	25	89	8	88	59	0	1	39	1.08
4937325--4937436	17	6.6	18	69	17	62	64	0	0	34	1.00
4937274--4937463	41	4.6	41	74	17	137	62	0	1	36	1.07
4937313--4937470	68	2.4	65	75	14	153	63	0	0	35	0.99
4939086--4939120	2	17.5	2	100	0	70	51	0	0	48	1.00
4939367--4939395	3	9.7	3	100	0	58	31	0	0	68	0.89
4943943--4944316	187	2.0	187	92	1	615	19	17	19	43	1.88
4945819--4945886	21	3.2	21	64	15	59	30	17	22	29	1.97
4945803--4945886	42	2.0	42	97	0	159	30	15	26	27	1.96
4952331--4952372	22	2.0	21	90	4	66	59	0	0	40	0.97
4956133--4956177	21	2.2	21	84	4	56	37	4	2	55	1.32
4958948--4958974	2	13.5	2	100	0	54	48	0	0	51	1.00
4960330--4960389	29	2.1	29	84	6	79	26	3	1	68	1.15
4960454--4960499	20	2.3	20	85	7	58	36	0	0	63	0.95
4961339--4961375	16	2.2	17	86	13	51	81	0	0	18	0.70
4961499--4961528	15	2.0	15	93	0	51	63	0	0	36	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4961970--4962001	2	16.0	2	100	0	64	50	50	0	0	1.00
4962425--4962474	15	3.5	14	75	20	50	56	2	0	42	1.11
4963401--4963435	7	5.0	7	100	0	70	28	14	28	28	1.95
4965512--4965564	15	3.6	14	75	7	52	52	5	0	41	1.25
4965835--4965867	2	16.5	2	100	0	66	51	0	0	48	1.00
4969437--4969532	2	51.0	2	71	12	60	58	1	0	40	1.05
4969414--4969502	29	3.0	30	76	15	96	56	0	1	42	1.06
4969432--4969532	41	2.5	42	80	13	131	59	0	0	39	1.04
4969432--4969531	39	2.5	40	82	9	125	60	1	0	39	1.04
4970166--4970212	20	2.4	19	82	6	58	55	0	6	38	1.26
4970168--4970248	35	2.3	35	81	8	94	55	0	7	37	1.28
4973580--4973621	21	2.0	21	90	4	68	57	0	0	42	0.99
4973949--4974003	22	2.5	22	81	3	65	43	0	1	54	1.10
4975040--4975079	2	20.0	2	100	0	80	50	0	0	50	1.00
4976459--4976526	27	2.4	30	80	11	81	41	0	0	58	0.98
4976510--4976612	16	6.4	16	67	16	52	38	2	1	56	1.26
4976557--4976600	22	2.0	23	90	4	72	38	2	0	59	1.10
4976510--4976586	16	4.7	17	71	27	60	38	2	2	55	1.27
4978398--4978423	2	13.0	2	100	0	52	50	0	0	50	1.00
4979586--4979646	16	3.9	15	81	10	68	52	0	4	42	1.23
4981195--4981253	4	14.8	4	85	7	75	76	0	3	20	0.93
4982113--4982177	30	2.2	30	78	8	71	35	7	4	52	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4982253--4982340	30	3.0	28	76	5	77	53	1	6	38	1.35
4987459--4987486	2	14.0	2	100	0	56	50	0	0	50	1.00
4990322--4990438	58	2.0	58	98	0	225	26	15	22	35	1.94
4990878--4990922	20	2.1	23	88	12	69	64	2	0	33	1.06
4991439--4991750	121	2.6	120	86	3	401	41	13	5	39	1.67
4993999--4994042	20	2.2	20	87	0	61	43	18	13	25	1.86
4994241--4994315	25	3.0	25	73	11	73	58	2	36	2	1.26
4994247--4994297	19	2.7	19	81	6	50	58	1	37	1	1.20
4994496--4994543	19	2.4	20	82	6	53	52	2	0	45	1.12
4995174--4995199	2	13.0	2	100	0	52	50	0	0	50	1.00
4997892--4997926	6	5.8	6	100	0	70	65	0	0	34	0.93
4998100--4998129	2	15.0	2	100	0	60	50	0	0	50	1.00
5000801--5000830	16	1.9	16	93	6	53	63	3	0	33	1.11
5001058--5001131	21	3.6	21	82	14	75	55	0	0	44	0.99
5003248--5003303	26	2.1	27	83	9	71	48	0	0	51	1.00
5003261--5003311	21	2.4	21	81	15	61	49	0	0	50	1.00
5003323--5003365	17	2.4	19	81	14	56	44	0	0	55	0.99
5004079--5004119	11	3.6	12	77	9	50	70	4	0	24	1.06
5004399--5004648	130	1.9	133	90	3	407	35	7	10	46	1.68
5005811--5005840	16	1.9	15	93	6	51	23	6	3	66	1.30
5010709--5010743	2	18.0	2	94	5	63	51	0	0	48	1.00
5014211--5014251	16	2.6	16	88	0	55	24	19	0	56	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5014630--5014706	28	3.0	24	78	12	66	46	23	9	20	1.79
5019167--5019212	24	1.9	25	91	8	78	45	26	8	19	1.79
5021873--5021910	20	1.9	20	89	10	60	76	2	5	15	1.08
5022913--5022966	25	2.2	25	89	0	81	1	20	5	72	1.14
5023513--5023563	19	2.7	19	84	6	59	60	3	35	0	1.15
5024041--5024115	20	3.8	20	78	0	87	34	13	12	40	1.81
5024041--5024118	40	2.0	39	87	2	111	34	12	12	39	1.82
5039947--5041399	32	46.2	32	92	3	2205	31	34	17	16	1.92
5041927--5042001	20	3.8	20	78	0	87	34	13	12	40	1.81
5041927--5042004	40	2.0	39	87	2	111	34	12	12	39	1.82
5045425--5045450	2	13.0	2	100	0	52	50	0	0	50	1.00
5045499--5045538	16	2.4	17	83	8	55	55	2	2	40	1.27
5046032--5046061	15	2.0	15	100	0	60	20	20	26	33	1.97
5050068--5050177	50	2.2	50	93	0	184	27	30	18	24	1.98
5051624--5051669	18	2.6	18	85	0	65	36	0	8	54	1.32
5052329--5052394	33	2.0	33	96	0	123	33	16	12	37	1.86
5053042--5053100	6	9.8	6	100	0	118	66	0	0	33	0.92
5055068--5055113	20	2.4	19	82	13	58	43	15	2	39	1.59
5055343--5055371	14	2.0	15	93	6	51	55	6	0	37	1.27
5055920--5056006	37	2.3	38	84	5	115	25	10	25	39	1.87
5055936--5056015	37	2.1	38	83	2	99	30	13	20	36	1.91
5060260--5060388	52	2.5	52	96	0	231	29	17	17	35	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5060260--5060408	52	2.9	51	89	4	219	30	16	18	34	1.93
5060397--5060421	13	1.9	13	100	0	50	36	16	16	32	1.90
5060487--5060511	13	1.9	13	100	0	50	32	16	16	36	1.90
5064282--5064365	37	2.3	37	87	0	123	28	19	21	30	1.97
5066062--5066098	14	2.6	14	86	0	56	43	0	18	37	1.51
5073668--5073697	6	5.2	6	96	4	53	46	0	0	53	1.00
5074669--5074722	27	1.9	27	81	7	63	50	0	0	50	1.00
5075758--5075794	20	1.9	20	94	5	67	43	0	0	56	0.99
5075753--5075797	20	2.4	18	86	13	65	44	0	0	55	0.99
5081544--5081600	22	2.6	22	97	0	105	22	0	36	40	1.55
5085821--5085903	35	2.4	35	85	2	105	22	2	37	37	1.68
5094217--5094280	29	2.2	29	88	0	92	53	6	7	32	1.55
5094400--5094535	21	6.3	21	74	8	103	48	8	8	35	1.62
5096419--5096452	17	2.1	16	88	5	50	85	11	0	2	0.71
5096804--5096923	21	5.7	21	80	5	116	52	8	3	35	1.48
5096804--5096909	10	10.0	11	69	20	59	50	8	3	36	1.51
5097821--5097955	34	4.0	34	93	0	225	36	10	25	28	1.89
5098898--5098930	11	3.1	11	86	4	50	42	0	3	54	1.15
5101693--5101726	2	17.0	2	100	0	68	50	0	0	50	1.00
5104204--5104255	11	4.7	12	77	22	60	53	5	0	40	1.25
5104230--5104370	20	7.0	20	69	15	71	53	9	2	34	1.48
5104316--5104370	9	5.3	11	71	20	55	54	7	1	36	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5104305--5104370	20	3.2	20	85	4	96	51	7	3	37	1.46
5104305--5104388	21	4.1	21	82	10	102	47	8	5	38	1.58
5104316--5104407	41	2.2	41	82	3	105	46	8	6	38	1.61
5104378--5104428	21	2.5	21	83	3	68	43	7	7	41	1.63
5104616--5104656	21	2.0	21	90	0	64	48	12	2	36	1.54
5104624--5104823	21	9.6	21	70	8	131	52	10	5	32	1.58
5104739--5104813	11	7.1	11	71	14	59	53	10	5	30	1.58
5105029--5105066	19	2.0	20	85	15	53	57	5	5	31	1.43
5105208--5105373	21	7.9	21	80	4	156	52	6	4	36	1.47
5105224--5105562	42	8.0	42	71	14	189	53	7	4	34	1.49

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