genome.fa.s90.2.7.7.80.10.50.1000.4.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: Scaffold90
Parameters: 2 7 7 80 10 50 1000
Length:  1653315

Tables:   1   2   3   4   5   6   7   8   9   10   

This is table  4  of  10  ( 1200 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)
376443--376511	35	1.9	36	85	5	95	23	14	17	44	1.85
376644--376742	47	2.1	48	90	1	155	39	3	23	34	1.70
377370--377421	20	2.6	20	87	6	70	36	13	11	38	1.81
378252--378297	17	2.7	17	80	6	58	17	2	4	76	1.06
379456--379709	40	6.5	39	68	10	142	31	15	11	42	1.82
379563--379786	79	2.8	77	75	9	200	30	15	12	41	1.84
381060--381129	15	4.9	14	71	13	54	64	0	0	35	0.94
382391--382444	17	3.3	17	70	17	51	51	0	0	48	1.00
382781--382865	11	7.7	11	72	20	63	68	3	3	24	1.22
382781--382865	22	3.8	22	79	4	91	68	3	3	24	1.22
383085--383128	17	2.7	16	83	13	54	56	0	0	43	0.99
383452--383511	23	2.7	21	76	23	61	71	5	1	21	1.14
383451--383510	12	5.2	12	76	13	63	71	5	1	21	1.14
383618--383674	30	1.9	30	82	7	71	5	22	0	71	1.05
383786--383818	11	2.8	12	90	9	59	63	0	9	27	1.24
383924--383985	20	3.0	21	80	7	63	59	6	1	32	1.32
384015--384064	22	2.4	20	86	6	64	62	0	0	38	0.96
390373--390406	17	2.0	17	100	0	68	58	11	17	11	1.62
399258--399365	21	5.3	18	66	30	58	10	48	1	39	1.48
399261--399379	42	2.8	42	93	0	202	9	46	1	42	1.46
399294--399369	12	6.9	11	75	15	52	9	48	2	39	1.49
401225--401250	13	2.0	13	100	0	52	30	15	15	38	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
401910--402053	61	2.4	61	97	2	272	24	31	6	38	1.80
402009--402052	21	2.1	21	83	8	54	25	31	4	38	1.76
403857--403882	13	2.0	13	100	0	52	38	15	15	30	1.88
405920--405950	15	2.1	15	93	0	53	12	22	16	48	1.80
407620--407664	21	2.1	21	84	8	56	22	20	4	53	1.63
409879--409904	13	2.0	13	100	0	52	30	15	15	38	1.88
420283--420382	19	5.9	19	73	25	98	36	12	14	38	1.83
420304--420360	13	3.9	13	76	24	60	35	14	15	35	1.88
420285--420379	32	3.0	32	96	0	172	35	12	14	36	1.85
420422--420447	13	2.0	13	100	0	52	30	15	15	38	1.88
420402--420468	33	2.0	33	88	0	98	25	14	16	43	1.86
422921--422955	17	2.1	17	88	0	52	31	37	17	14	1.89
423019--423091	27	2.6	28	81	12	89	24	32	20	21	1.97
422941--423145	107	1.9	107	88	1	313	27	27	14	29	1.95
435647--435712	11	5.8	11	75	10	53	81	6	12	0	0.85
435654--435692	20	1.9	21	89	5	62	87	10	2	0	0.65
435654--435693	15	2.6	14	88	7	53	87	10	2	0	0.63
436729--436814	27	3.1	27	62	15	68	27	30	18	23	1.98
436679--437301	55	11.3	55	89	5	922	28	29	20	21	1.98
439979--440023	21	2.1	21	84	8	56	53	4	20	22	1.63
441819--441849	15	2.1	15	93	0	53	48	16	22	12	1.80
443703--443727	8	3.1	8	100	0	50	16	0	24	60	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
443925--443950	13	2.0	13	100	0	52	30	15	15	38	1.88
447897--447953	21	2.7	21	88	0	87	35	8	17	38	1.81
450870--450942	19	3.7	20	85	5	94	32	15	17	34	1.91
450980--451042	32	2.0	32	90	0	99	36	12	12	38	1.82
450979--451045	19	3.8	19	70	22	65	37	11	11	38	1.79
453583--453615	17	1.9	17	93	0	57	24	39	21	15	1.91
453678--453750	27	2.6	28	81	12	89	24	32	20	21	1.97
453599--453825	106	2.1	107	88	0	330	26	26	16	30	1.96
460784--460901	12	10.9	11	72	19	63	40	1	47	10	1.47
460774--460864	33	2.8	30	77	12	76	43	1	45	9	1.44
460804--460864	9	7.1	9	72	10	56	42	1	44	11	1.50
460783--460934	42	3.6	42	95	0	268	41	1	46	9	1.48
460849--460919	18	3.6	18	71	20	61	45	2	43	8	1.49
467945--468009	29	2.1	33	83	11	84	32	3	0	64	1.09
469752--469785	2	17.0	2	93	0	59	50	0	2	47	1.16
470264--470303	12	3.3	12	85	0	53	5	70	0	25	1.08
472372--472499	41	3.1	41	87	0	175	27	8	5	58	1.50
472394--472465	22	3.4	21	73	19	78	27	6	5	59	1.46
472394--472456	19	3.2	19	72	12	63	28	4	6	60	1.42
472406--472472	22	3.2	22	75	12	77	29	5	7	56	1.51
475856--475880	13	1.9	13	100	0	50	32	16	16	36	1.90
475962--476010	20	2.5	20	87	9	66	38	18	16	26	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
484095--484144	20	2.5	20	86	0	64	36	22	14	28	1.92
484226--484251	13	2.0	13	100	0	52	38	15	15	30	1.88
484208--484271	33	2.0	32	84	9	85	40	18	12	28	1.87
485733--485809	38	2.0	38	100	0	154	33	10	5	50	1.59
488779--488803	13	1.9	13	100	0	50	36	16	16	32	1.90
488788--488844	19	3.0	20	74	7	64	35	14	15	35	1.88
488889--488919	13	2.4	13	94	0	53	35	16	9	38	1.81
488873--488940	33	2.1	33	88	5	102	32	13	16	38	1.87
495063--495115	13	4.1	13	90	0	79	30	13	15	41	1.85
497632--497656	13	1.9	13	100	0	50	36	16	16	32	1.90
497611--497675	33	2.0	32	88	8	96	30	15	15	38	1.88
497641--497693	19	2.8	20	80	8	65	33	13	16	35	1.88
497742--497794	13	4.5	13	73	26	64	32	13	16	37	1.88
497726--497794	33	2.1	33	91	5	113	30	13	18	37	1.89
500187--500233	23	2.0	23	83	8	58	31	6	0	61	1.21
500203--500291	44	2.0	44	87	8	128	25	6	7	59	1.50
505220--505683	238	1.9	238	93	0	802	30	12	18	39	1.87
507035--507059	13	1.9	13	100	0	50	36	16	16	32	1.90
507047--507112	20	3.7	20	71	26	74	40	15	16	27	1.88
507035--507113	33	2.4	33	97	0	149	40	15	16	27	1.88
514868--516957	49	43.8	49	72	11	1202	32	17	25	24	1.97
514761--515842	351	3.1	351	96	1	1920	34	15	25	23	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
515764--516957	137	8.7	137	73	13	470	30	18	25	25	1.98
515716--516076	186	1.9	185	86	1	508	32	18	25	23	1.97
516046--516216	88	2.0	87	82	3	209	29	17	26	25	1.97
515665--516770	235	4.8	235	90	2	1580	31	17	25	25	1.97
516653--516899	39	5.9	39	71	19	183	27	20	25	26	1.99
516692--516947	48	5.7	48	71	17	226	28	20	25	25	1.99
516519--516952	87	5.0	87	88	0	616	29	19	24	26	1.98
517015--517098	30	2.8	30	78	3	98	22	15	29	32	1.95
517097--517195	33	3.2	33	77	16	120	38	11	29	21	1.88
517119--517218	27	3.5	27	83	15	137	31	13	33	23	1.92
517097--517253	60	2.6	60	87	2	215	36	12	29	21	1.90
517166--517449	125	2.3	125	81	7	328	35	14	28	21	1.93
517165--517452	94	3.1	91	81	8	323	36	14	28	21	1.92
517228--517449	31	7.2	30	83	7	257	35	14	28	21	1.93
518726--518771	6	7.8	6	85	9	60	2	0	13	84	0.71
518714--518772	11	5.3	11	80	10	57	3	0	13	83	0.78
518716--518778	19	3.2	19	82	11	56	4	1	12	80	0.93
518712--518779	31	2.2	31	76	7	77	5	2	13	77	1.06
528098--528151	21	2.5	22	96	3	101	61	9	11	18	1.55
529064--529134	20	3.5	20	80	3	72	39	11	14	35	1.81
529698--530796	57	19.0	57	84	6	1317	22	17	31	28	1.97
529698--530795	28	38.0	29	84	6	1288	22	17	31	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
532009--532048	20	2.1	20	86	9	57	5	7	5	82	0.94
545109--545164	22	2.5	23	97	2	105	62	8	10	17	1.52
546076--546146	20	3.5	20	82	3	81	40	11	12	35	1.79
619435--619489	26	2.1	26	100	0	110	41	7	18	32	1.78
620237--620288	27	2.0	26	84	3	68	42	3	5	48	1.45
620567--620760	107	1.8	105	85	5	273	45	4	8	41	1.55
621356--621398	22	2.0	22	90	4	70	51	9	2	37	1.47
621969--622674	353	2.0	353	99	0	1387	33	20	11	34	1.89
627199--627358	44	3.7	43	80	6	171	51	10	14	23	1.73
627231--627358	41	3.0	42	80	5	168	52	10	14	23	1.71

Tables:   1   2   3   4   5   6   7   8   9   10