genome.fa.s4.2.7.7.80.10.50.1000.12.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  12  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)
2779998--2780350	150	2.4	150	91	0	564	20	25	13	41	1.88
2784375--2784979	258	2.4	247	78	14	663	42	20	14	22	1.88
2784746--2785445	222	3.0	219	81	8	711	42	20	14	23	1.88
2785438--2785499	9	6.9	9	77	0	61	53	19	9	17	1.71
2785438--2785499	27	2.3	27	88	0	97	53	19	9	17	1.71
2785551--2785594	9	4.9	9	88	0	70	50	20	11	18	1.77
2786030--2786119	30	3.0	30	91	0	144	14	43	14	27	1.84
2787227--2787260	18	1.9	18	88	5	52	67	0	0	32	0.91
2787226--2787269	19	2.4	18	81	11	54	65	0	0	34	0.93
2789007--2789065	21	2.7	21	82	15	75	40	11	1	45	1.51
2789484--2789638	63	2.4	64	78	10	149	30	7	6	55	1.53
2790073--2790459	68	5.6	69	75	13	280	54	8	8	29	1.59
2790998--2791035	18	2.1	18	90	0	58	55	2	2	39	1.28
2791834--2791881	21	2.2	22	82	10	64	70	4	0	25	1.04
2792078--2792124	10	4.1	11	81	13	51	31	0	0	68	0.90
2792074--2792153	26	3.0	28	72	7	76	41	0	0	58	0.98
2792074--2792141	27	2.6	27	79	6	77	39	0	0	60	0.97
2792080--2792128	14	3.5	15	71	21	52	32	0	0	67	0.91
2792389--2792440	26	2.1	26	85	7	72	50	0	0	50	1.00
2792387--2792445	26	2.5	22	74	15	55	50	0	0	49	1.00
2792592--2792636	23	2.0	23	83	12	58	44	2	2	51	1.26
2793652--2793691	21	1.9	21	90	10	64	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2793834--2793916	29	2.9	31	76	16	83	43	0	0	56	0.99
2793855--2793907	22	2.3	23	80	6	63	41	0	0	58	0.98
2793845--2793916	29	2.6	29	86	6	96	43	0	0	56	0.99
2798079--2798126	2	23.5	2	91	4	69	50	6	0	43	1.27
2799997--2800042	13	3.3	13	80	16	56	65	0	0	34	0.93
2800295--2800349	18	2.9	19	86	2	76	50	0	1	47	1.11
2800288--2800382	41	2.5	38	81	10	106	50	0	4	45	1.21
2800303--2800382	41	1.9	42	87	2	117	51	0	3	45	1.19
2800334--2800421	31	2.8	30	80	10	88	53	0	3	43	1.17
2800405--2800455	22	2.3	21	80	6	57	54	0	0	45	0.99
2800518--2800590	19	3.7	19	72	21	60	49	0	0	50	1.00
2800604--2800655	27	1.9	27	92	0	86	65	3	0	30	1.10
2800639--2800704	28	2.5	26	75	18	64	59	1	0	39	1.07
2800773--2800836	24	2.7	23	76	4	65	50	0	0	50	1.00
2801882--2801929	19	2.5	19	82	3	51	45	0	0	54	0.99
2802761--2802797	17	2.2	17	95	0	65	5	21	2	70	1.20
2803752--2803792	19	2.2	19	86	8	57	56	2	0	41	1.13
2804319--2804343	13	1.9	13	100	0	50	68	0	0	32	0.90
2804761--2805022	144	1.8	146	86	2	386	47	9	8	34	1.66
2805102--2805164	31	2.0	32	84	3	83	58	3	6	31	1.39
2805286--2805362	32	2.5	30	78	17	86	61	2	0	36	1.10
2805288--2805363	31	2.5	30	83	10	91	60	2	0	36	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2805360--2805413	14	3.7	13	76	23	54	0	16	1	81	0.78
2806289--2806343	20	2.8	20	85	0	65	63	0	3	32	1.12
2822465--2822609	72	2.0	72	100	0	290	38	24	8	28	1.84
2824643--2824706	26	2.4	27	86	5	85	39	0	1	59	1.07
2824671--2824722	19	2.6	19	80	14	61	38	0	1	59	1.08
2824900--2824944	23	2.0	23	86	0	63	24	2	4	68	1.19
2827459--2827490	13	2.3	15	89	10	50	56	21	3	18	1.56
2828072--2828102	3	10.3	3	92	0	53	67	3	0	29	1.06
2828894--2828980	14	5.9	14	70	21	54	57	0	2	40	1.11
2828935--2828971	18	2.1	18	90	5	58	62	0	0	37	0.96
2834927--2834982	2	28.5	2	81	3	60	46	5	1	46	1.36
2843197--2843235	12	3.2	12	85	3	51	56	2	0	41	1.13
2843197--2843230	13	2.7	13	86	4	52	52	0	0	47	1.00
2843689--2843756	16	4.2	17	75	16	63	47	0	0	52	1.00
2844863--2844892	15	1.9	16	93	6	53	83	0	16	0	0.65
2845471--2845495	2	12.5	2	100	0	50	52	0	0	48	1.00
2847186--2847222	3	12.7	3	94	5	67	32	0	0	67	0.91
2847355--2847388	15	2.3	15	95	5	61	64	0	0	35	0.94
2847524--2847554	2	15.5	2	93	0	53	51	0	0	48	1.00
2849106--2849150	9	4.7	10	76	17	51	37	0	0	62	0.96
2849086--2849144	20	3.1	19	80	9	57	37	0	3	59	1.14
2849117--2849167	13	4.0	12	80	19	59	33	0	1	64	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2849125--2849168	11	3.7	11	77	16	52	34	0	2	63	1.07
2849125--2849183	25	2.3	26	88	2	93	37	0	1	61	1.07
2849161--2849194	15	2.3	15	89	0	50	47	0	0	52	1.00
2850229--2850258	2	15.0	2	92	0	51	46	0	0	53	1.00
2850744--2850776	3	11.0	3	100	0	66	66	0	0	33	0.92
2853464--2853496	15	2.1	16	88	5	50	51	9	21	18	1.73
2855746--2855792	23	2.1	22	88	7	69	36	0	8	55	1.31
2857939--2858014	27	2.8	28	71	15	68	42	1	0	56	1.07
2858419--2858490	11	6.2	12	72	22	55	51	0	0	48	1.00
2858431--2858490	18	3.4	17	76	17	59	51	0	0	48	1.00
2859338--2859362	2	12.5	2	100	0	50	48	0	0	52	1.00
2864337--2864377	20	2.0	20	100	0	82	19	19	9	51	1.74
2872275--2872317	13	3.3	13	83	9	52	37	0	0	62	0.95
2872286--2872324	18	2.1	19	85	4	53	35	0	0	64	0.94
2872337--2872405	18	3.9	19	71	24	62	50	0	0	49	1.00
2872351--2872398	16	3.1	15	74	11	51	52	0	0	47	1.00
2872337--2872416	32	2.4	34	85	10	103	47	1	0	51	1.08
2872329--2872404	32	2.6	28	78	15	91	50	0	0	50	1.00
2872732--2872775	21	2.1	21	87	8	63	25	61	0	13	1.32
2873383--2873418	2	18.0	2	88	0	54	47	2	2	47	1.31
2875235--2875265	2	15.5	2	100	0	62	48	0	0	51	1.00
2888139--2888163	2	12.5	2	100	0	50	48	0	52	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2888598--2888801	99	2.1	99	99	0	399	35	20	22	22	1.96
2892611--2892654	2	22.0	2	90	0	70	54	0	45	0	0.99
2896979--2897011	16	2.1	16	94	0	57	42	9	12	36	1.74
2899294--2899328	15	2.2	16	90	5	54	0	11	2	85	0.69
2905878--2905931	12	4.4	13	79	11	60	50	0	0	50	1.00
2906264--2906294	4	8.0	4	92	7	55	74	0	0	25	0.82
2909036--2909083	24	2.0	24	100	0	96	45	20	16	16	1.85
2909433--2909462	14	2.2	13	94	5	51	66	0	0	33	0.92
2909865--2909921	27	2.1	28	83	9	73	42	3	3	50	1.36
2911303--2911330	14	2.0	14	100	0	56	21	57	7	14	1.61
2912318--2912408	45	2.0	45	95	0	164	28	24	10	36	1.89
2916909--2916983	16	4.6	16	74	12	64	56	0	0	44	0.99
2922706--2922771	18	3.7	18	73	16	57	56	3	0	40	1.15
2922715--2922770	18	3.1	18	76	7	60	58	3	0	37	1.15
2923378--2923409	3	10.7	3	100	0	64	68	0	0	31	0.90
2926100--2926128	2	14.5	2	100	0	58	48	0	0	51	1.00
2929066--2929117	23	2.3	23	86	3	70	65	0	1	32	1.04
2929093--2929125	13	2.3	15	90	10	52	63	0	0	36	0.95
2933622--2933660	18	2.2	18	85	0	51	66	2	2	28	1.18
2934040--2934140	50	2.0	50	96	0	184	42	16	20	19	1.89
2939216--2939246	14	2.3	13	94	5	53	0	12	0	87	0.55
2940235--2940305	21	3.3	21	69	11	54	42	0	1	56	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2940253--2940328	37	2.1	37	85	5	100	43	0	1	55	1.08
2940290--2940360	9	7.3	9	71	20	54	38	0	0	61	0.96
2940234--2940304	6	10.1	7	70	22	51	40	0	1	57	1.07
2940270--2940340	30	2.4	30	82	17	94	43	0	0	56	0.99
2940294--2940350	19	2.8	20	78	5	62	40	0	0	59	0.97
2940298--2940351	20	2.7	20	80	11	65	38	0	0	61	0.96
2942712--2942769	30	1.9	30	86	6	82	50	6	0	43	1.29
2943168--2943244	16	4.5	17	74	19	52	41	0	0	58	0.98
2944159--2944199	6	7.0	6	83	10	50	46	17	34	2	1.61
2944159--2944200	18	2.4	18	84	4	59	45	16	35	2	1.61

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