genome.fa.s129.2.7.7.80.10.50.1000.20.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: Scaffold129
Parameters: 2 7 7 80 10 50 1000
Length:  3652842

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   

This is table  20  of  23  ( 2702 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)
3108528--3108583	21	2.8	21	75	5	62	39	14	12	33	1.83
3114185--3114555	124	3.0	124	96	0	661	59	8	19	13	1.59
3115612--3115655	13	3.5	13	93	3	72	25	18	9	47	1.77
3115756--3115911	64	2.4	64	87	4	217	19	28	14	37	1.91
3115871--3115950	33	2.4	33	85	8	110	16	31	12	40	1.85
3116111--3116194	37	2.3	37	81	4	107	17	20	14	47	1.82
3116487--3116573	31	2.8	30	74	19	88	28	27	27	16	1.97
3116646--3116718	31	2.4	31	81	4	85	28	23	27	20	1.99
3116487--3116926	149	3.0	148	81	6	501	29	23	24	22	1.99
3116782--3116862	31	2.6	31	78	3	92	30	25	20	22	1.98
3117417--3117505	20	4.7	20	75	14	80	41	13	15	29	1.85
3117435--3117464	15	2.0	15	100	0	60	40	13	13	33	1.83
3118602--3118635	12	2.8	12	90	0	50	44	26	11	17	1.83
3122256--3122832	157	3.6	160	73	12	456	36	22	17	24	1.95
3122283--3122907	318	2.0	317	81	4	742	36	21	17	24	1.94
3122231--3122938	318	2.2	315	78	6	741	37	21	16	24	1.94
3124685--3124763	14	6.1	12	72	19	52	63	2	1	32	1.16
3124685--3124734	15	3.6	15	76	17	54	68	2	0	30	1.01
3125066--3125137	19	3.4	19	73	19	63	61	1	2	34	1.19
3125673--3125701	12	2.4	12	100	0	58	72	13	0	13	1.13
3127223--3127250	13	2.2	13	100	0	56	32	14	14	39	1.86
3127204--3127272	33	2.1	33	84	10	88	31	11	17	39	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3128685--3128766	36	2.3	36	95	0	146	40	23	15	20	1.91
3133558--3133607	21	2.4	22	83	9	61	32	20	0	48	1.50
3136031--3136055	13	1.9	13	100	0	50	32	8	16	44	1.76
3136012--3136080	33	2.1	33	86	0	93	28	11	20	39	1.87
3136973--3137364	41	9.5	42	70	5	224	35	13	31	18	1.90
3136961--3137363	125	3.2	124	74	7	379	36	12	32	18	1.89
3137639--3137902	42	6.3	42	77	4	138	36	17	27	18	1.93
3137703--3138017	127	2.5	127	82	5	354	37	18	26	17	1.93
3137703--3138017	42	7.5	41	78	6	238	37	18	26	17	1.93
3138285--3138451	89	1.9	89	82	5	212	29	16	26	26	1.97
3139387--3139711	111	2.9	109	79	8	296	36	14	19	30	1.91
3139991--3140023	9	3.7	9	84	15	50	3	18	0	78	0.87
3139990--3140024	18	1.9	18	100	0	70	5	17	0	77	0.96
3140257--3140328	11	6.5	10	73	17	54	5	16	2	75	1.12
3141151--3141182	16	2.0	16	93	0	55	18	9	37	34	1.83
3143964--3144624	160	4.2	158	73	8	492	37	21	18	22	1.94
3147835--3147896	32	1.9	33	86	3	90	30	16	12	40	1.86
3149466--3149512	3	16.0	3	91	4	78	36	0	31	31	1.58
3152402--3152890	28	17.2	28	88	2	611	22	17	31	28	1.97
3157070--3157172	52	2.0	52	84	3	136	33	17	16	33	1.92
3157219--3157281	19	3.7	18	72	24	64	36	19	11	33	1.87
3157211--3157281	32	2.2	32	94	0	124	36	19	11	32	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3158016--3158281	98	2.7	101	81	8	278	33	18	24	24	1.97
3158016--3158303	52	5.7	51	79	10	279	33	17	24	24	1.96
3158016--3158303	150	1.9	151	85	5	402	33	17	24	24	1.96
3158324--3158521	49	4.0	49	84	4	227	32	16	27	23	1.96
3158538--3158633	28	3.4	28	83	11	131	15	14	34	35	1.88
3160074--3160197	1	124.0	1	73	0	95	0	2	10	86	0.71
3160074--3160199	12	10.8	12	76	18	115	0	2	11	85	0.73
3160074--3160197	23	5.4	23	77	12	121	0	2	10	86	0.71
3165389--3165415	13	2.1	13	100	0	54	7	14	25	51	1.68
3174205--3174261	19	3.3	18	72	27	61	38	17	12	31	1.87
3174218--3174242	13	1.9	13	100	0	50	32	16	16	36	1.90
3174191--3174261	32	2.2	32	92	0	115	38	16	11	33	1.85
3174230--3174283	19	2.8	18	77	20	63	33	16	14	35	1.90
3174648--3174727	36	2.2	35	80	10	90	6	8	6	78	1.08
3181946--3181982	2	18.5	2	100	0	74	48	0	0	51	1.00
3188155--3188229	20	3.8	19	78	7	87	38	14	14	32	1.87
3188152--3188229	40	2.0	39	89	2	120	38	15	14	32	1.87
3188907--3188941	17	2.1	17	100	0	70	40	17	5	37	1.73
3189460--3189503	20	2.1	21	91	4	72	61	20	0	18	1.35
3193406--3193855	184	2.5	181	86	3	607	41	9	8	41	1.66
3196065--3196251	52	3.6	52	88	1	241	42	11	18	27	1.85
3196065--3196253	104	1.8	104	88	2	290	42	11	17	27	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3196322--3196347	13	2.0	13	100	0	52	30	7	15	46	1.74
3203537--3203722	97	1.9	97	82	4	232	39	11	21	27	1.88
3203589--3203773	97	1.9	97	81	4	221	39	10	22	27	1.86
3204586--3204611	13	2.0	13	100	0	52	30	15	15	38	1.88
3204565--3204629	32	2.0	34	90	6	107	27	12	15	44	1.82
3204681--3204736	20	2.8	20	89	5	78	28	17	16	37	1.91
3207148--3207185	13	2.9	13	96	0	67	31	15	18	34	1.92
3207174--3207304	20	7.6	20	63	31	88	45	12	15	26	1.81
3207161--3207307	33	4.5	33	100	0	294	43	12	15	28	1.83
3207194--3207218	13	1.9	13	100	0	50	32	16	16	36	1.90
3207227--3207251	13	1.9	13	100	0	50	32	16	16	36	1.90
3207260--3207284	13	1.9	13	100	0	50	32	16	16	36	1.90
3209366--3209396	15	2.1	15	93	0	53	12	22	16	48	1.80
3213466--3213491	13	2.0	13	100	0	52	30	15	15	38	1.88
3213445--3213509	32	2.0	34	90	6	107	27	12	15	44	1.82
3213561--3213616	20	2.8	20	83	5	69	30	16	16	37	1.90
3214336--3214376	22	1.9	21	95	5	73	51	0	17	31	1.46
3213979--3214780	404	2.0	404	93	0	1381	40	12	17	29	1.87
3216498--3216544	20	2.3	20	96	0	85	57	10	6	25	1.56
3216601--3216654	20	2.7	20	76	2	54	31	12	11	44	1.78
3219268--3219481	97	2.2	97	85	5	290	29	23	11	35	1.90
3221423--3221584	40	3.8	40	72	19	146	29	16	12	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3221423--3221494	20	3.6	19	79	7	81	31	13	12	41	1.82
3221511--3221584	20	3.7	20	79	0	94	31	16	13	39	1.87
3221410--3221584	91	1.9	90	92	1	296	29	17	12	41	1.86
3226972--3227012	14	2.9	14	79	13	57	14	0	14	70	1.16
3231948--3231992	24	1.9	23	86	4	63	71	8	0	20	1.12
3233566--3233614	2	25.0	2	95	4	91	48	0	0	51	1.00
3234663--3234701	2	19.5	2	100	0	78	48	0	0	51	1.00
3235211--3235262	17	3.0	17	91	2	77	30	25	3	40	1.73
3236861--3236916	11	5.1	11	74	8	51	32	1	5	60	1.29
3236860--3236916	22	2.5	22	88	2	78	31	1	5	61	1.28
3240147--3240275	52	2.5	52	93	0	222	29	19	17	34	1.94
3240147--3240295	52	2.9	51	80	9	176	31	18	16	32	1.94
3240281--3240308	13	2.2	13	100	0	56	39	17	14	28	1.89
3240349--3240412	32	2.0	33	93	3	112	35	14	12	37	1.83
3241167--3241472	49	6.2	49	75	11	259	34	16	24	24	1.95
3241137--3241328	102	1.9	105	84	5	266	34	16	22	25	1.95
3241380--3241467	43	2.0	43	88	0	131	31	18	23	26	1.97
3241535--3241826	29	10.0	29	85	4	381	24	16	30	29	1.96
3241530--3241825	59	5.1	58	89	1	414	24	15	30	29	1.96
3241530--3241825	117	2.5	116	89	2	441	24	15	30	29	1.96
3243342--3243404	20	3.3	19	85	10	83	0	17	1	80	0.78
3243342--3243404	19	3.3	19	83	12	76	0	17	1	80	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3248250--3248370	52	2.3	52	97	0	224	28	18	18	34	1.94
3248250--3248390	52	2.7	51	90	4	212	30	17	18	33	1.94
3248379--3248403	13	1.9	13	100	0	50	36	16	16	32	1.90
3248444--3248510	33	2.0	33	88	0	98	40	13	11	34	1.81
3248466--3248490	13	1.9	13	100	0	50	32	16	16	36	1.90
3249417--3250381	49	19.7	49	94	1	1571	31	18	25	24	1.97
3249408--3250381	244	4.0	243	94	1	1606	31	17	25	24	1.97
3250374--3250452	33	2.5	31	80	11	106	18	16	37	26	1.92
3250387--3250450	33	1.9	34	96	3	121	18	18	34	28	1.95
3250455--3250864	34	12.6	32	77	15	266	32	13	33	20	1.91

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23