genome.fa.s25.2.7.7.80.10.50.1000.16.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  16  of  56  ( 6609 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)
3023761--3023851	45	2.0	47	95	4	168	36	2	5	56	1.35
3027047--3027091	10	4.5	11	78	18	53	46	0	0	53	1.00
3027116--3027156	21	1.9	22	90	5	66	39	0	0	60	0.96
3027068--3027140	29	2.6	28	76	19	82	41	0	0	58	0.98
3029616--3029646	2	15.5	2	100	0	62	51	0	0	48	1.00
3031678--3031712	16	2.1	17	89	10	54	60	0	0	40	0.97
3032006--3032069	5	12.4	5	76	12	58	60	1	0	37	1.06
3032002--3032064	11	5.4	11	78	12	54	61	0	0	38	0.96
3032006--3032073	16	4.4	16	75	18	56	60	1	0	38	1.06
3032006--3032064	22	2.5	22	86	8	73	61	0	0	38	0.96
3033252--3033283	4	8.0	4	100	0	64	25	0	25	50	1.50
3042979--3043044	30	2.1	32	88	5	100	56	0	0	43	0.99
3042801--3043052	110	2.3	108	87	4	357	51	0	2	44	1.19
3047131--3047475	87	3.9	90	85	6	381	35	15	7	41	1.75
3047323--3047628	155	2.0	155	85	3	420	34	16	7	41	1.77
3047478--3047878	85	4.7	86	83	5	451	34	16	6	41	1.75
3047478--3048316	174	5.0	172	74	11	524	35	16	6	41	1.75
3047737--3048041	153	2.0	154	81	9	356	34	15	5	43	1.71
3047564--3048208	324	2.0	333	83	5	823	35	15	6	41	1.74
3047150--3048296	411	2.8	414	84	5	1392	35	15	7	41	1.75
3047888--3048294	87	4.7	88	76	7	341	36	15	6	41	1.74
3049044--3049073	15	2.0	15	93	0	51	36	0	0	63	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3049044--3049285	125	1.9	129	84	10	327	42	2	1	53	1.20
3049051--3049309	126	2.1	123	81	13	295	42	2	1	53	1.22
3049079--3049331	125	2.0	123	80	11	282	43	2	1	52	1.21
3049991--3050040	9	6.0	9	88	9	54	44	0	0	56	0.99
3051846--3051889	2	22.0	2	100	0	88	50	0	0	50	1.00
3052149--3052189	15	2.7	15	88	0	64	58	0	0	41	0.98
3052297--3052341	18	2.4	18	81	3	54	46	0	0	53	1.00
3052387--3052415	15	2.0	15	93	6	51	55	6	0	37	1.27
3053145--3053195	15	3.3	15	81	10	66	33	0	1	64	1.05
3053132--3053175	22	2.0	23	90	4	72	34	0	4	61	1.16
3053145--3053203	16	3.7	16	81	0	73	33	0	3	62	1.12
3053284--3053315	16	2.0	16	93	0	55	34	0	0	65	0.93
3053544--3053578	2	17.5	2	100	0	70	51	0	0	48	1.00
3056015--3056062	15	3.1	16	80	20	57	58	0	0	41	0.98
3056278--3056312	3	11.7	3	93	0	61	62	0	2	34	1.10
3056964--3057040	25	3.1	25	73	12	59	46	0	1	51	1.09
3057153--3057185	2	16.5	2	100	0	66	51	0	0	48	1.00
3058916--3058956	2	21.0	2	85	5	57	48	2	2	46	1.28
3059515--3059563	26	2.0	26	88	11	77	51	0	0	48	1.00
3060402--3060434	13	2.4	14	95	5	59	39	0	0	60	0.97
3061983--3062007	2	12.5	2	100	0	50	0	52	0	48	1.00
3064525--3064551	2	13.5	2	100	0	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)
3065968--3066076	44	2.5	44	77	14	109	51	0	0	48	1.00
3066009--3066043	18	1.9	18	88	0	52	60	0	0	40	0.97
3066052--3066089	20	1.9	20	89	10	60	52	0	0	47	1.00
3066400--3066441	10	4.3	10	78	6	50	35	9	2	52	1.47
3066404--3066440	19	1.9	19	88	0	56	37	10	2	48	1.52
3066490--3066541	20	2.5	21	79	17	63	40	0	1	57	1.10
3066501--3066526	12	2.2	12	100	0	52	38	0	0	61	0.96
3066802--3066883	41	2.0	41	100	0	164	19	29	4	46	1.71
3068738--3068996	99	2.6	98	83	3	322	21	28	21	28	1.99
3068738--3068996	33	7.8	33	84	0	277	21	28	21	28	1.99
3075112--3075144	14	2.4	14	90	5	50	75	0	0	24	0.80
3074890--3075236	184	1.9	184	92	0	586	46	3	7	42	1.48
3075548--3075593	20	2.2	21	88	3	67	41	0	2	56	1.11
3076929--3076984	27	2.0	28	82	3	69	48	1	1	48	1.22
3076983--3077018	14	2.8	14	80	20	51	72	0	0	27	0.85
3079815--3079848	17	2.0	17	88	0	50	44	0	5	50	1.26
3081511--3081597	39	2.3	37	80	7	95	48	0	0	51	1.00
3081787--3081812	2	13.0	2	100	0	52	50	0	0	50	1.00
3085562--3085667	6	18.7	6	69	16	50	38	1	0	59	1.08
3085581--3085638	20	2.7	21	81	10	64	44	0	0	55	0.99
3088109--3088216	54	2.0	55	83	1	137	32	13	22	31	1.93
3090860--3090897	19	2.1	18	90	5	58	57	0	0	42	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3091553--3091582	16	1.9	16	93	6	53	46	0	0	53	1.00
3091642--3091694	21	2.5	21	84	9	63	58	0	0	41	0.98
3092204--3092248	5	9.4	5	81	18	60	37	0	0	62	0.96
3097266--3097308	22	1.9	23	90	4	70	44	0	0	55	0.99
3097445--3097479	17	2.0	18	88	5	54	45	5	0	48	1.26
3097452--3097492	21	2.0	21	85	9	57	41	7	0	51	1.30
3098729--3098817	11	8.1	11	71	15	51	37	1	2	59	1.17
3098771--3098815	13	3.4	14	79	11	51	37	0	2	60	1.09
3098800--3098838	11	3.5	11	82	0	51	28	0	0	71	0.86
3099059--3099085	2	13.5	2	100	0	54	51	0	0	48	1.00
3099985--3100021	19	1.9	19	94	0	65	13	13	35	37	1.84
3100414--3100512	11	9.3	10	70	23	53	64	2	1	32	1.11
3103601--3103634	15	2.2	15	89	5	50	20	2	14	61	1.46
3104707--3104737	16	1.9	16	93	0	53	70	0	0	29	0.87
3110189--3110238	21	2.4	21	83	9	59	58	2	0	40	1.10
3110245--3110278	17	2.1	16	88	5	50	38	0	0	61	0.96
3111128--3111169	9	4.7	9	82	5	50	35	2	0	61	1.09
3111800--3111838	10	3.8	10	89	3	60	58	2	10	28	1.44
3112764--3112893	44	2.9	44	80	1	107	36	16	13	33	1.88
3119897--3119946	17	2.8	18	76	11	50	26	16	2	56	1.51
3123317--3123363	20	2.3	21	85	3	60	36	0	0	63	0.94
3123332--3123391	15	3.8	15	78	18	59	41	0	1	56	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3123338--3123404	32	2.0	35	91	8	113	41	0	2	55	1.15
3124217--3124247	16	2.0	16	93	6	55	41	0	6	51	1.27
3125254--3125306	20	2.7	20	73	2	54	54	13	0	32	1.39
3126260--3126288	14	2.0	15	93	6	51	55	3	0	41	1.17
3126273--3126326	17	3.1	18	78	7	58	46	0	0	53	1.00
3127787--3127830	14	2.9	15	83	10	63	56	0	0	43	0.99
3128580--3128652	38	1.9	38	83	10	96	43	1	1	53	1.17
3132862--3132914	27	2.0	27	88	0	79	33	11	11	43	1.76
3139820--3139867	14	3.5	13	78	15	53	56	6	2	35	1.36
3140310--3140345	15	2.4	15	90	0	54	38	0	0	61	0.96
3142125--3142181	29	1.9	29	82	10	71	47	1	0	50	1.11
3142129--3142212	30	2.8	31	81	15	88	48	1	0	50	1.08
3142140--3142221	29	2.8	30	81	16	86	48	0	0	51	1.00
3143083--3143138	23	2.4	23	85	8	69	51	1	8	37	1.44
3146561--3146589	2	15.0	2	92	7	51	48	0	0	51	1.00
3150973--3151015	21	2.0	21	81	0	50	44	0	2	53	1.13
3153515--3153540	6	4.3	6	100	0	52	15	0	0	84	0.62
3153606--3153639	15	2.2	16	89	5	52	50	0	0	50	1.00
3161991--3162032	21	2.0	20	86	4	57	35	0	2	61	1.09
3162225--3162278	26	2.0	28	82	10	67	50	0	0	50	1.00
3163437--3163475	20	2.0	20	85	10	53	33	12	10	43	1.77
3164990--3165020	16	1.9	16	93	0	53	70	0	0	29	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3165088--3165127	18	2.2	18	86	13	55	62	0	0	37	0.95
3166750--3166780	16	1.9	16	100	0	62	51	0	3	45	1.17
3166757--3166810	18	2.8	20	74	20	53	46	0	3	50	1.19
3167215--3167254	19	2.0	21	85	9	57	42	2	5	50	1.37
3167713--3167754	16	2.6	16	82	17	52	33	0	2	64	1.07
3168589--3168640	28	1.9	26	85	14	70	55	1	11	30	1.46
3169574--3169603	15	1.9	16	93	6	53	43	0	0	56	0.99
3171582--3171656	28	2.6	28	81	10	80	62	5	1	30	1.25
3171769--3171806	3	12.7	3	100	0	76	68	0	0	31	0.90
3172564--3172594	6	5.2	6	100	0	62	51	32	0	16	1.44

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   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56