genome.fa.s125.2.7.7.80.10.50.1000.17.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: Scaffold125
Parameters: 2 7 7 80 10 50 1000
Length:  3608436

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   

This is table  17  of  18  ( 2131 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)
3154862--3154897	2	18.0	2	88	0	54	44	0	5	50	1.25
3157466--3157506	2	21.0	2	95	5	75	48	0	0	51	1.00
3158433--3158479	14	3.4	14	80	11	51	57	0	0	42	0.98
3158443--3158479	13	2.6	15	87	12	60	59	0	0	40	0.97
3158448--3158512	30	2.1	32	82	5	80	55	0	0	44	0.99
3163352--3163400	20	2.5	20	96	0	89	77	4	4	14	1.06
3163674--3163698	6	4.2	6	100	0	50	80	0	0	20	0.72
3165291--3165323	2	16.5	2	100	0	66	51	0	0	48	1.00
3165401--3165437	15	2.4	16	82	13	51	51	0	0	48	1.00
3166054--3166091	10	3.9	10	82	3	51	47	0	0	52	1.00
3166079--3166121	13	3.1	15	83	16	65	60	0	0	39	0.97
3166867--3166899	2	16.5	2	100	0	66	51	0	0	48	1.00
3167224--3167272	24	2.0	24	84	7	64	38	2	0	59	1.09
3168122--3168154	17	1.9	18	88	11	52	48	3	0	48	1.17
3169334--3169364	15	2.1	14	94	5	53	22	0	0	77	0.77
3173427--3173465	20	2.0	20	89	0	60	28	28	10	33	1.90
3174668--3174713	15	2.9	15	81	12	56	47	0	0	52	1.00
3176295--3176339	19	2.4	18	85	10	56	4	13	2	80	0.97
3177623--3177749	63	2.0	63	96	0	236	37	9	11	41	1.73
3186310--3186374	33	2.0	32	85	8	87	41	0	0	58	0.98
3188532--3188583	19	2.6	20	82	14	63	55	0	0	44	0.99
3190347--3190423	37	2.1	37	87	0	109	51	3	27	16	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3190579--3190606	2	14.0	2	100	0	56	50	0	0	50	1.00
3191456--3191510	24	2.3	24	100	0	110	38	18	7	36	1.78
3196173--3196203	3	10.3	3	100	0	62	67	0	0	32	0.91
3196591--3196627	2	18.5	2	100	0	74	48	0	0	51	1.00
3202620--3202695	22	3.5	22	75	12	59	36	3	1	57	1.25
3202764--3203004	126	1.9	126	83	0	313	40	4	7	46	1.55
3202987--3203059	30	2.5	31	80	10	91	60	0	0	39	0.97
3203166--3203201	18	2.1	18	89	5	56	41	0	0	58	0.98
3206658--3206747	44	2.0	44	97	0	171	35	16	13	34	1.88
3206914--3207027	57	2.0	57	96	0	210	18	7	21	52	1.70
3208086--3208132	16	2.9	17	81	9	62	34	0	2	63	1.06
3209549--3209662	17	6.3	17	69	20	54	51	2	0	44	1.21
3211675--3211744	23	3.0	23	72	14	63	70	4	0	25	1.06
3215541--3215576	14	2.5	14	95	4	63	58	0	0	41	0.98
3217103--3217130	3	9.3	3	100	0	56	32	0	0	67	0.91
3218674--3218743	11	6.8	11	73	18	62	35	1	0	62	1.04
3218658--3218787	39	3.2	39	68	25	92	37	1	0	60	1.06
3218661--3218799	28	5.1	26	75	15	113	37	1	0	61	1.05
3218763--3218797	12	3.0	12	87	8	54	37	0	0	62	0.95
3220337--3220396	2	30.0	2	96	0	111	48	0	1	50	1.11
3224763--3224806	17	2.7	17	86	6	56	43	2	0	54	1.12
3231634--3231663	15	2.1	14	93	6	51	0	10	0	90	0.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3232908--3232969	23	2.8	22	73	4	63	58	1	1	38	1.18
3233684--3233719	7	5.0	7	90	6	54	16	2	0	80	0.83
3236815--3236843	2	14.5	2	100	0	58	51	0	0	48	1.00
3238801--3238871	25	2.9	23	76	21	72	52	0	1	46	1.09
3241802--3241845	19	2.5	18	82	13	56	54	0	0	45	0.99
3242259--3242284	2	13.0	2	100	0	52	50	0	0	50	1.00
3242955--3242986	2	16.0	2	93	0	55	46	0	3	50	1.17
3250384--3250426	12	3.7	12	87	3	61	48	6	0	44	1.29
3250838--3250871	15	2.3	15	90	5	52	55	0	0	44	0.99
3263332--3263379	3	16.0	3	100	0	96	66	0	0	33	0.92
3265429--3265462	16	2.1	16	100	0	68	29	26	20	23	1.99
3270194--3270268	23	3.2	24	75	14	68	41	0	1	57	1.07
3270194--3270279	46	1.9	44	84	13	113	39	0	1	59	1.05
3270767--3270796	16	1.9	15	93	6	51	50	3	0	46	1.18
3270875--3270923	22	2.3	22	86	10	66	40	0	0	59	0.98
3279333--3279367	17	2.2	16	90	10	54	28	2	0	68	1.04
3280388--3280457	23	3.2	22	76	13	65	30	2	1	65	1.15
3285117--3285157	12	3.4	12	96	0	73	53	0	46	0	1.00
3285150--3285184	15	2.3	15	90	0	52	34	0	57	8	1.29
3286758--3286797	3	13.7	3	89	5	64	67	0	0	32	0.91
3286750--3286797	23	2.1	23	88	0	69	66	4	0	29	1.10
3286761--3286802	20	2.0	21	90	4	68	69	0	0	30	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3286757--3286805	20	2.5	20	81	15	66	69	0	0	30	0.89
3286758--3286805	17	2.9	17	80	17	57	68	0	0	31	0.90
3288892--3288916	4	6.2	4	100	0	50	28	0	0	72	0.86
3291110--3291145	2	18.0	2	100	0	72	50	0	0	50	1.00
3291433--3291465	15	2.3	15	89	5	50	63	0	6	30	1.18
3291518--3291547	15	2.0	15	93	0	51	50	0	0	50	1.00
3291695--3291747	14	3.6	14	87	5	70	30	0	1	67	1.01
3292573--3292614	2	21.0	2	90	9	68	47	0	2	50	1.14
3303453--3303530	21	3.5	21	68	21	61	42	0	0	57	0.98
3303457--3303540	15	5.4	15	74	8	62	44	0	0	55	0.99
3303461--3303545	26	3.0	27	76	20	75	47	0	0	52	1.00
3303484--3303567	32	2.6	32	85	9	100	45	0	0	54	0.99
3303535--3303585	24	2.1	25	85	3	68	39	0	0	60	0.97
3312846--3313063	34	6.5	34	84	5	273	40	26	7	25	1.82
3312844--3313063	67	3.3	67	87	1	314	40	26	7	25	1.82
3317474--3317689	34	6.4	34	84	5	269	40	26	7	25	1.83
3317472--3317689	67	3.2	67	87	1	310	40	27	7	24	1.82
3318930--3318978	24	2.0	24	84	7	64	57	4	2	36	1.30
3322526--3322570	3	15.0	3	100	0	90	33	0	0	66	0.92
3324559--3324603	23	2.0	23	86	0	63	57	0	2	40	1.11
3324570--3324624	23	2.3	24	81	12	69	54	3	1	40	1.28
3325453--3325501	3	16.3	3	86	0	71	67	2	2	28	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3328327--3328352	12	2.2	12	100	0	52	30	0	7	61	1.24
3333376--3333409	2	17.0	2	100	0	68	50	0	0	50	1.00
3333780--3333838	18	3.3	19	79	9	54	50	1	0	47	1.11
3334643--3334797	34	4.6	34	83	4	172	30	7	22	39	1.82
3339205--3339423	34	6.5	34	85	2	271	26	7	25	40	1.82
3339205--3339422	102	2.1	101	90	2	339	26	7	25	40	1.82
3343595--3343645	23	2.2	24	85	3	68	45	0	0	54	0.99
3343683--3343721	19	2.1	19	85	0	51	76	2	10	10	1.10
3344092--3344133	16	2.6	16	84	0	57	54	0	0	45	0.99
3344845--3344877	16	2.0	17	94	5	59	54	0	0	45	0.99
3347771--3347810	2	20.0	2	94	0	71	0	47	0	52	1.00
3351043--3351075	2	17.0	2	93	6	59	51	0	0	48	1.00
3351420--3351477	18	3.2	17	76	11	62	63	0	0	36	0.94
3352727--3352767	14	2.9	15	82	7	50	36	0	4	58	1.20
3352783--3352815	13	2.6	13	90	4	50	51	0	0	48	1.00
3354271--3354348	39	2.0	39	82	0	93	48	3	7	39	1.50
3354325--3354819	165	3.0	162	84	4	582	41	7	17	34	1.77
3355715--3355742	13	2.2	13	100	0	56	21	21	14	42	1.88
3356233--3356460	111	2.1	111	94	0	393	36	11	17	33	1.86
3359160--3359215	26	2.1	27	83	9	71	33	0	3	62	1.12
3359160--3359226	21	3.1	22	77	14	68	35	0	4	59	1.18
3361483--3361525	22	2.0	22	86	9	61	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3361748--3362066	155	2.1	153	82	6	367	48	13	5	32	1.66
3361915--3362208	139	2.1	138	87	4	421	48	12	6	31	1.67
3362359--3362388	15	2.0	15	93	0	51	3	13	0	83	0.77
3362381--3362425	23	2.0	23	86	0	63	2	24	0	73	0.95
3363249--3363295	14	3.4	13	78	21	51	61	2	0	36	1.08
3363243--3363295	28	1.9	27	88	11	81	60	1	0	37	1.08
3363243--3363295	16	3.6	16	73	17	60	60	1	0	37	1.08
3367196--3367239	17	2.4	18	81	11	54	56	0	2	40	1.11
3370022--3370076	16	3.1	18	77	17	53	45	0	1	52	1.11
3370208--3370276	31	2.2	31	84	5	86	37	0	0	62	0.96

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18