genome.fa.s4.2.7.7.80.10.50.1000.13.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  13  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)
2944312--2944361	23	2.1	24	82	10	59	48	0	0	52	1.00
2944326--2944389	30	2.1	31	82	8	78	50	0	1	48	1.10
2944364--2944403	20	2.0	20	85	5	53	45	0	2	52	1.14
2945739--2945764	2	13.0	2	100	0	52	0	50	0	50	1.00
2946979--2947040	32	1.9	33	86	3	90	61	1	0	37	1.06
2946975--2947059	29	2.7	31	80	10	86	61	2	0	36	1.09
2952013--2952061	17	2.9	17	81	9	64	0	30	2	67	1.02
2952309--2952338	15	2.0	15	93	0	51	50	0	0	50	1.00
2952391--2952417	13	2.1	13	100	0	54	22	22	7	48	1.75
2952555--2952587	2	16.5	2	100	0	66	0	51	0	48	1.00
2954591--2954632	9	4.4	10	88	8	52	69	0	0	30	0.89
2954978--2955015	18	2.1	18	85	9	51	44	2	2	50	1.30
2960796--2960841	24	2.0	23	87	8	67	45	0	0	54	0.99
2962392--2962428	2	18.5	2	100	0	74	51	0	0	48	1.00
2968127--2968184	17	3.5	17	72	13	57	27	0	25	46	1.53
2968283--2968327	13	3.5	13	100	0	90	33	0	0	66	0.92
2968280--2968343	26	2.5	24	79	16	76	31	0	3	65	1.08
2968313--2968420	17	6.4	17	69	18	64	42	0	2	54	1.14
2968284--2968374	9	9.6	10	69	20	54	34	0	1	64	1.01
2968457--2968502	17	2.8	16	81	12	58	60	0	0	39	0.97
2969011--2969041	2	16.0	2	93	6	55	48	0	0	51	1.00
2971107--2971160	25	2.3	23	84	12	67	35	0	1	62	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2971107--2971172	22	2.9	24	79	14	61	34	0	4	60	1.17
2971169--2971225	18	3.2	19	85	11	68	52	0	0	47	1.00
2971183--2971225	17	2.5	17	85	10	61	48	0	0	51	1.00
2971183--2971230	17	2.9	16	79	11	60	45	0	0	54	0.99
2972036--2972088	22	2.4	22	84	6	72	43	0	0	56	0.99
2974444--2974478	3	11.7	3	100	0	70	65	0	0	34	0.93
2975147--2975194	2	24.0	2	100	0	96	50	0	0	50	1.00
2976028--2976072	22	2.0	22	91	0	72	68	0	2	28	1.01
2976051--2976127	32	2.4	32	86	6	102	57	3	2	36	1.31
2976816--2976866	24	2.0	26	92	7	88	66	0	0	33	0.92
2977937--2977971	10	3.5	10	88	0	52	54	0	2	42	1.15
2981438--2981469	2	16.0	2	100	0	64	50	0	0	50	1.00
2981816--2981854	15	2.6	15	79	0	51	28	10	5	56	1.54
2990617--2990739	19	6.6	19	67	17	53	46	1	0	51	1.16
2990670--2990745	36	2.1	37	92	5	127	42	5	0	52	1.24
2990682--2990739	17	3.3	17	71	17	55	43	3	0	53	1.17
2991144--2991181	15	2.5	15	87	8	51	42	2	0	55	1.14
2993453--2993491	20	2.0	20	85	10	53	56	0	0	43	0.99
2993544--2993595	17	3.1	17	80	8	61	42	1	0	55	1.10
2993647--2993715	36	1.9	35	82	11	86	55	0	0	44	0.99
2993669--2993718	27	1.9	27	92	8	86	58	0	0	42	0.98
2998852--2998882	5	6.2	5	100	0	62	58	22	0	19	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3000038--3000110	22	3.2	22	66	16	58	52	0	0	47	1.00
3000037--3000147	46	2.4	47	90	4	172	49	0	0	49	1.07
3005299--3005360	22	2.8	23	78	7	74	61	0	0	38	0.96
3010582--3010633	26	2.0	27	84	3	70	59	0	0	40	0.97
3010628--3011016	210	1.9	209	96	0	645	37	16	20	26	1.93
3011938--3011976	20	2.0	20	90	10	62	30	0	2	66	1.05
3011937--3012002	29	2.3	28	84	5	87	33	0	1	65	1.02
3018773--3018828	18	3.2	18	80	14	64	58	0	0	41	0.98
3023310--3023415	29	3.7	28	76	15	85	62	0	0	36	1.02
3023908--3023940	17	1.9	17	93	0	57	69	3	0	27	1.03
3024470--3024537	21	3.1	22	76	6	66	44	1	1	52	1.19
3024510--3024542	9	3.8	9	84	8	50	42	0	0	57	0.98
3024510--3024542	17	1.9	17	93	0	57	42	0	0	57	0.98
3024724--3024756	16	2.1	16	94	0	57	36	21	3	39	1.69
3029080--3029119	19	2.1	19	85	0	53	65	0	0	35	0.93
3029035--3029115	35	2.3	35	82	8	92	58	1	2	38	1.20
3029093--3029165	19	3.7	19	71	18	60	57	1	0	41	1.07
3029131--3029199	27	2.6	27	71	11	70	57	0	0	42	0.98
3030381--3030434	25	2.1	26	83	10	67	55	0	1	42	1.10
3030883--3030924	22	1.9	22	85	9	59	59	0	2	38	1.10
3035641--3035789	71	2.1	71	98	0	289	26	24	10	38	1.88
3036860--3036957	42	2.3	41	85	3	124	29	10	35	24	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3043289--3043372	42	2.0	42	86	4	116	25	16	14	44	1.85
3047443--3047467	2	12.5	2	100	0	50	0	48	0	52	1.00
3048332--3048378	25	1.9	25	82	4	60	31	12	4	51	1.59
3048926--3048981	21	2.7	21	75	10	51	51	1	12	33	1.50
3053254--3053322	19	3.6	18	75	7	57	27	1	1	69	1.05
3053512--3053551	21	1.9	21	85	10	55	40	15	2	42	1.60
3053663--3053933	143	2.0	138	89	8	421	39	10	14	35	1.81
3059752--3059792	2	20.5	2	89	0	64	51	4	0	43	1.23
3061601--3061636	2	18.0	2	100	0	72	50	0	0	50	1.00
3063944--3063983	2	20.0	2	100	0	80	50	0	0	50	1.00
3066379--3066439	28	2.2	28	79	5	70	42	0	1	55	1.09
3070278--3070311	2	17.0	2	100	0	68	0	50	0	50	1.00
3072863--3072902	17	2.3	18	86	4	55	30	0	5	65	1.14
3081171--3081202	2	16.0	2	93	0	55	53	0	0	46	1.00
3089062--3089124	29	2.2	30	83	11	78	38	4	0	57	1.20
3089105--3089152	16	2.8	16	77	22	53	43	2	0	54	1.12
3089180--3089204	11	2.3	11	100	0	50	44	0	0	56	0.99
3093222--3093291	20	3.4	22	77	13	69	64	0	0	35	0.94
3093228--3093286	25	2.3	27	80	13	72	64	0	0	35	0.94
3093246--3093336	32	2.9	31	82	12	105	60	0	0	39	0.97
3093280--3093341	20	3.5	19	72	28	64	53	0	0	46	1.00
3093280--3093327	15	2.9	16	77	17	53	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3093280--3093341	18	3.5	17	79	16	65	53	0	0	46	1.00
3093248--3093384	20	6.5	20	64	21	57	57	0	0	42	0.98
3093310--3093406	43	2.3	42	79	10	99	55	2	1	41	1.18
3096927--3097145	34	6.5	34	89	2	300	40	26	7	25	1.81
3096925--3097145	102	2.2	101	89	1	343	40	27	7	24	1.81
3098640--3098822	34	5.4	34	86	3	244	39	27	7	25	1.82
3100812--3100838	2	13.5	2	100	0	54	48	0	0	51	1.00
3104986--3105039	25	2.2	25	96	0	99	29	14	14	40	1.86
3116095--3116125	16	1.9	16	93	0	53	54	0	0	45	0.99
3116495--3116527	2	16.5	2	93	0	57	48	0	0	51	1.00
3118684--3118718	17	2.1	17	89	5	54	28	2	0	68	1.04
3120285--3120313	2	14.5	2	100	0	58	0	51	0	48	1.00
3122464--3122537	13	5.8	13	79	6	53	75	0	24	0	0.80
3122486--3122540	29	2.0	29	86	10	80	81	0	18	0	0.68
3122471--3122536	4	16.8	4	83	12	57	77	0	22	0	0.77
3123209--3123241	17	1.9	17	93	0	57	36	6	24	33	1.80
3127249--3127467	34	6.5	34	89	2	300	40	26	7	25	1.81
3127247--3127467	102	2.2	101	89	1	343	40	27	7	24	1.81
3128959--3129141	34	5.4	34	86	3	244	39	27	7	25	1.82
3131135--3131190	2	28.5	2	96	3	105	48	0	0	51	1.00
3135331--3135384	25	2.2	25	96	0	99	29	14	14	40	1.86
3149016--3149054	17	2.4	17	87	8	55	28	2	0	69	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3150623--3150652	2	15.0	2	100	0	60	0	50	0	50	1.00
3152807--3152861	4	13.8	4	81	14	60	72	0	27	0	0.85
3152819--3152864	15	3.2	15	84	9	69	78	0	21	0	0.76
3152806--3152864	28	2.1	27	87	9	84	74	0	25	0	0.82
3153527--3153559	17	1.9	17	93	0	57	36	6	24	33	1.80
3160997--3161034	15	2.5	15	91	0	58	31	2	31	34	1.72
3165521--3165604	43	2.0	43	97	0	159	11	15	11	60	1.58
3169388--3169419	2	16.0	2	100	0	64	50	0	0	50	1.00
3179770--3179938	91	1.9	91	85	5	234	28	20	15	35	1.93
3183508--3183553	24	2.0	23	86	4	65	45	4	4	45	1.43

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