genome.fa.s4.2.7.7.80.10.50.1000.25.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  25  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)
5105448--5105539	21	4.4	21	73	5	87	56	5	1	36	1.30
5105524--5105579	20	2.8	20	91	0	85	44	7	1	46	1.41
5105655--5105697	20	2.2	20	91	0	68	55	6	6	30	1.53
5105660--5105706	20	2.4	19	86	10	60	57	6	8	27	1.53
5105691--5105921	21	11.1	21	71	9	125	50	11	5	33	1.60
5105871--5105921	20	2.5	21	80	6	68	52	7	1	37	1.42
5105913--5105951	19	2.1	18	95	4	69	51	0	12	35	1.40
5109826--5109867	20	2.1	20	90	0	66	35	16	4	42	1.69
5110655--5110714	28	2.1	28	90	6	95	35	8	10	46	1.67
5110824--5110892	29	2.4	30	69	23	51	39	0	2	57	1.13
5110882--5110948	21	3.2	21	73	12	66	50	0	2	46	1.16
5112078--5112126	14	3.2	14	80	13	53	44	0	0	55	0.99
5112078--5112126	16	2.9	18	72	27	54	44	0	0	55	0.99
5112445--5112486	16	2.5	17	81	11	52	61	2	2	33	1.21
5112721--5112771	4	12.8	4	81	8	59	0	25	0	74	0.82
5112713--5112775	12	4.9	12	73	21	56	0	23	0	76	0.79
5113604--5113636	16	2.0	17	94	5	59	27	0	0	72	0.85
5113604--5113641	8	4.3	9	81	18	53	31	0	0	68	0.90
5113835--5113873	17	2.1	18	86	13	53	74	5	2	17	1.12
5114152--5114212	12	5.4	12	73	15	58	63	1	0	34	1.04
5114143--5114216	31	2.4	29	81	16	87	63	2	0	33	1.09
5114270--5114321	6	8.5	6	85	10	70	0	19	0	80	0.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5114394--5114454	32	1.9	32	83	12	81	62	0	6	31	1.21
5114415--5114462	23	2.2	20	85	10	60	66	0	2	31	1.03
5114429--5114467	11	3.5	11	85	3	51	64	0	5	30	1.15
5114568--5114677	11	10.2	11	73	13	52	65	1	0	32	1.03
5114580--5114680	26	3.8	25	76	8	67	64	1	0	33	1.05
5114579--5114645	21	3.2	20	78	16	73	65	2	0	31	1.07
5114578--5114709	37	3.5	38	74	18	100	65	2	0	31	1.05
5114616--5114709	32	2.8	34	78	13	90	65	2	0	31	1.04
5114725--5114761	4	9.8	4	85	11	51	0	24	0	75	0.80
5114722--5114761	15	2.7	15	92	0	62	0	22	0	77	0.77
5114729--5114762	11	3.1	11	82	0	50	0	23	0	76	0.79
5114900--5114984	13	6.0	15	73	15	74	56	0	1	42	1.07
5114909--5114998	30	3.3	27	71	17	78	57	0	1	41	1.06
5114993--5115026	17	2.0	17	88	0	50	64	2	2	29	1.22
5115008--5115057	24	2.1	24	88	7	75	64	6	0	30	1.18
5115972--5116035	4	16.5	4	77	6	60	0	23	0	76	0.79
5116907--5117015	37	3.0	36	75	18	120	60	4	0	34	1.17
5116924--5117008	33	2.6	34	78	14	106	63	3	0	32	1.11
5118966--5119074	54	2.0	55	85	1	148	40	12	8	38	1.74
5119432--5119476	17	2.7	17	79	3	56	55	0	2	42	1.12
5119432--5119479	16	2.9	16	78	6	60	58	0	2	39	1.10
5119906--5119943	10	3.9	10	79	6	51	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5120380--5120427	25	2.0	25	88	8	73	52	2	0	45	1.12
5120720--5120755	14	2.6	14	91	8	56	38	2	0	58	1.13
5120997--5121047	26	2.0	26	88	0	75	47	0	1	50	1.12
5121005--5121047	12	3.4	13	84	12	54	48	0	0	51	1.00
5121759--5121943	34	5.5	34	86	0	255	26	7	25	40	1.82
5122248--5122310	19	3.3	19	90	0	90	28	17	19	34	1.94
5126376--5126560	34	5.5	34	88	0	264	25	7	26	40	1.82
5127985--5128019	18	1.9	18	94	0	61	28	5	8	57	1.52
5129926--5129970	20	2.3	19	88	3	63	40	0	0	60	0.97
5129926--5129978	20	2.7	20	77	11	56	39	0	0	60	0.97
5129974--5129999	11	2.4	11	100	0	52	53	0	0	46	1.00
5130461--5130501	20	2.0	20	86	9	57	58	0	0	41	0.98
5137353--5137377	13	1.9	13	100	0	50	48	0	0	52	1.00
5137495--5137560	31	2.1	32	91	2	107	60	7	3	28	1.39
5138717--5138812	16	6.0	16	76	13	99	23	14	19	41	1.89
5138723--5138809	32	2.7	31	84	10	122	24	13	18	43	1.86
5139197--5139235	2	19.5	2	94	0	69	48	0	0	51	1.00
5145430--5145467	20	1.9	20	89	10	60	39	2	0	57	1.12
5145820--5145878	20	2.9	20	72	18	59	66	1	0	32	1.02
5147703--5148045	171	2.0	171	100	0	686	20	26	13	38	1.90
5148204--5148319	57	2.0	57	98	0	223	12	21	21	43	1.86
5151486--5151561	24	3.2	23	74	20	68	36	0	2	60	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5151522--5151585	30	2.1	31	83	13	80	37	0	1	60	1.06
5151555--5151604	23	2.2	23	85	7	66	42	0	4	54	1.19
5159569--5159609	20	2.0	20	86	9	57	58	19	14	7	1.59
5162459--5162483	2	12.5	2	100	0	50	48	0	0	52	1.00
5164314--5164361	2	24.0	2	100	0	96	50	0	0	50	1.00
5164583--5164655	26	2.8	26	79	8	78	49	0	0	50	1.00
5165089--5165159	27	2.7	26	80	6	79	57	0	1	40	1.07
5164992--5165327	168	2.0	167	97	0	636	51	5	6	36	1.52
5165260--5165327	27	2.6	26	81	9	75	55	0	1	42	1.08
5165261--5165342	27	3.1	26	75	18	71	54	0	1	43	1.07
5166113--5166168	20	2.8	20	81	8	60	50	1	0	48	1.11
5166172--5166223	19	2.5	21	77	20	56	42	1	1	53	1.23
5166196--5166241	17	2.7	18	80	16	53	34	2	2	60	1.21
5167026--5167070	2	23.5	2	78	17	51	44	2	0	53	1.13
5167048--5167091	16	2.8	16	80	13	54	31	0	0	68	0.90
5167618--5167649	13	2.3	15	89	10	50	68	0	25	6	1.12
5167925--5167974	17	3.1	17	72	16	52	44	0	2	54	1.11
5169236--5169288	26	2.1	26	86	6	74	50	0	3	45	1.19
5170713--5170763	24	2.3	21	75	18	50	45	3	0	50	1.20
5171196--5171228	4	8.5	4	86	6	50	51	3	0	45	1.16
5171413--5171457	22	2.0	24	83	12	60	42	4	0	53	1.21
5171507--5171566	24	2.4	25	75	5	59	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5171658--5171699	21	2.0	21	90	0	66	38	0	0	61	0.96
5175322--5175363	16	2.6	17	81	7	52	38	0	0	61	0.96
5177057--5177102	12	3.8	12	82	8	58	30	0	2	67	1.03
5177049--5177103	23	2.3	24	84	9	69	36	0	1	61	1.06
5177585--5177625	21	2.0	20	90	4	64	51	0	0	48	1.00
5178805--5178879	36	2.2	36	81	13	88	53	1	2	42	1.23
5182866--5182914	24	2.2	24	82	10	59	46	8	4	40	1.52
5183145--5183217	34	2.1	34	80	9	78	75	10	8	5	1.18
5183471--5183516	24	2.0	24	86	4	67	6	17	0	76	1.00
5184778--5185251	32	14.8	32	93	1	745	16	18	33	31	1.93
5185234--5186465	27	45.0	27	91	2	1951	28	14	34	22	1.94
5187516--5187545	15	2.0	15	100	0	60	0	0	13	86	0.57
5193718--5193766	24	2.2	24	82	10	59	46	8	4	40	1.52
5193995--5194068	36	2.1	34	80	14	80	77	10	6	5	1.13
5194322--5194367	24	2.0	24	86	4	67	6	17	0	76	1.00
5195183--5195240	1	58.0	1	78	0	53	6	5	0	87	0.65
5198157--5198212	28	2.0	28	82	6	69	44	0	0	55	0.99
5198193--5198232	11	3.7	11	83	3	55	27	0	2	70	1.01
5199546--5199577	16	1.9	16	93	6	55	68	0	3	28	1.04
5199913--5199943	16	1.9	16	93	0	53	58	0	3	38	1.15
5201131--5201289	50	3.2	49	90	3	228	30	21	18	29	1.97
5205683--5205891	50	4.2	50	90	2	294	30	19	18	31	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5211344--5211408	32	2.0	32	82	5	78	50	3	6	40	1.43
5213943--5214009	23	2.9	23	79	2	71	29	4	5	59	1.41
5214189--5214350	21	7.7	21	68	9	71	35	3	7	53	1.47
5214241--5214324	22	3.9	23	74	13	79	38	3	5	52	1.43
5214443--5214521	20	3.8	20	75	8	68	29	1	11	58	1.41
5214529--5214590	17	3.4	18	79	16	65	38	0	6	54	1.26
5214577--5214624	18	2.5	19	80	6	53	43	0	2	54	1.12
5214585--5214681	39	2.5	39	72	14	92	46	0	1	52	1.07
5214635--5214681	22	2.1	22	84	11	60	46	0	0	53	1.00
5215540--5215596	16	3.7	15	75	15	53	54	0	0	45	0.99

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