genome.fa.s339.2.7.7.80.10.50.1000.4.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: Scaffold339
Parameters: 2 7 7 80 10 50 1000
Length:  1314099

Tables:   1   2   3   4   5   6   7   8   9   

This is table  4  of  9  ( 1034 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)
446918--447050	50	2.6	51	88	3	189	39	15	18	27	1.90
447862--448101	101	2.4	100	85	2	293	31	15	25	27	1.96
447754--448101	52	6.9	49	73	6	212	32	16	24	26	1.96
448169--448382	32	6.7	32	80	6	220	16	18	33	32	1.93
448233--448388	62	2.5	64	83	5	183	16	17	36	29	1.92
448563--448633	28	2.6	28	86	6	92	26	22	25	25	2.00
449986--450129	5	29.6	5	77	14	124	2	2	12	83	0.83
449978--450124	26	5.9	23	76	19	102	2	2	12	82	0.83
449977--450129	20	7.7	19	79	14	141	1	2	12	83	0.85
449992--450176	45	4.0	45	74	15	137	4	3	10	81	0.97
449990--450129	1	140.0	1	69	0	73	2	2	12	83	0.82
449986--450174	20	9.1	20	75	16	138	4	3	10	82	0.93
456574--456612	20	2.0	19	90	5	60	38	23	7	30	1.83
456601--456626	13	2.0	13	100	0	52	30	15	15	38	1.88
456696--456749	21	2.7	21	83	13	69	38	14	14	31	1.87
462810--462847	13	2.9	13	96	0	67	31	15	18	34	1.92
464703--464751	24	2.1	24	88	3	73	34	0	30	34	1.58
471588--471643	13	4.8	13	73	24	54	33	14	16	35	1.88
471694--471718	13	1.9	13	100	0	50	36	16	16	32	1.90
471674--471738	33	2.0	33	87	6	96	35	15	16	32	1.91
480032--480090	21	2.8	21	87	5	75	42	5	10	42	1.60
480200--480252	20	2.6	21	79	8	65	32	16	13	37	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
483498--483522	13	1.9	13	100	0	50	32	16	16	36	1.90
484132--484355	49	4.6	49	87	2	317	32	18	24	25	1.97
484151--484358	98	2.1	98	93	0	355	32	16	25	25	1.96
484425--485095	34	20.2	33	83	7	788	35	12	32	19	1.90
484436--485179	66	11.2	65	85	7	804	34	12	32	19	1.90
484425--485153	100	7.2	100	86	4	884	34	12	32	19	1.90
485158--485216	30	2.0	30	100	0	118	23	18	33	23	1.97
486154--486212	14	4.3	14	79	10	50	0	6	8	84	0.77
486532--486571	17	2.4	16	91	4	62	0	0	15	85	0.61
486532--486571	19	2.2	18	90	4	62	0	0	15	85	0.61
492123--492172	25	2.0	25	100	0	100	36	16	16	32	1.90
501103--502049	28	33.6	28	83	5	849	27	31	15	25	1.95
501136--501754	55	11.3	55	85	2	805	25	31	14	27	1.95
501723--503966	32	73.2	32	82	7	1875	31	29	18	20	1.97
504093--504271	48	3.8	48	84	1	225	21	26	16	35	1.94
504093--504271	95	1.9	95	84	0	241	21	26	16	35	1.94
508955--509013	20	3.0	20	89	0	82	42	11	11	33	1.78
508956--509026	20	3.5	20	88	3	81	40	15	12	30	1.85
512018--512540	164	3.2	160	82	6	574	49	9	9	32	1.67
512089--512651	164	3.5	159	81	8	476	49	8	8	32	1.65
520953--521000	25	2.0	24	84	15	64	50	4	0	45	1.21
522305--522428	53	2.3	54	80	6	144	42	19	8	29	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
522446--522502	16	3.5	16	72	11	53	45	19	14	21	1.85
522645--522708	22	2.7	23	73	9	58	54	0	1	43	1.09
522645--523123	100	4.7	103	72	13	328	46	5	3	44	1.44
529493--529536	23	1.9	23	100	0	88	31	4	18	45	1.69
530692--530726	2	17.5	2	100	0	70	48	0	0	51	1.00
531493--531544	2	26.0	2	100	0	104	50	0	0	50	1.00
535161--535269	45	2.4	45	98	0	209	32	33	6	28	1.82
540168--540243	31	2.4	32	82	10	86	30	2	6	60	1.36
540192--540243	16	3.3	16	79	15	63	30	0	7	61	1.24
543099--543137	21	2.0	20	90	10	62	35	15	10	38	1.81
543901--543951	14	3.7	13	82	10	57	78	0	15	5	0.93
544610--544828	58	3.8	57	75	4	181	24	13	12	49	1.77
544609--544828	116	1.9	116	79	7	250	24	13	13	49	1.77
544725--544878	58	2.7	57	82	8	161	28	11	9	50	1.69
544779--544869	29	3.1	29	72	12	80	30	9	9	49	1.69
544797--544878	29	2.8	31	74	10	82	31	10	8	48	1.68
544812--545034	116	1.9	116	79	8	249	27	12	15	44	1.82
544796--545021	58	3.9	57	75	9	197	27	11	15	45	1.81
556255--556501	97	2.5	97	84	1	343	29	12	28	29	1.93
558131--558176	14	3.2	14	81	12	58	17	0	2	80	0.81
558131--558176	5	9.6	5	81	15	53	17	0	2	80	0.81
558131--558180	23	2.2	23	89	7	75	18	0	2	80	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
558833--559324	52	9.8	50	78	6	396	33	16	25	24	1.96
559346--559530	32	5.8	32	80	8	198	18	18	31	30	1.96
559346--559537	65	3.0	65	81	8	207	19	18	31	30	1.95
559346--559531	96	1.9	96	84	6	252	18	18	31	30	1.96
559787--559878	33	2.8	32	77	12	87	35	14	30	19	1.91
559801--559966	83	2.0	83	87	0	242	30	13	32	22	1.93
559883--560203	99	3.2	99	78	7	294	35	12	31	20	1.90
559958--560238	132	2.1	132	84	5	354	35	12	31	20	1.90
559883--560450	100	5.7	98	77	9	389	33	11	32	22	1.90
559966--560223	66	3.9	65	78	11	249	35	12	31	20	1.89
560252--560451	106	1.9	105	86	3	285	32	11	33	23	1.90
560370--560451	32	2.5	32	84	4	92	35	14	30	19	1.92
560394--560486	32	2.9	32	84	6	109	34	13	25	25	1.94
560407--560537	30	4.2	31	75	8	106	35	13	25	25	1.93
561782--561808	10	2.7	10	100	0	54	7	7	0	85	0.75
566316--566553	97	2.5	97	88	2	370	29	13	28	28	1.94
566758--566795	19	2.0	19	94	0	67	13	31	13	42	1.82
567449--567496	19	2.5	19	86	0	69	10	22	37	29	1.88
567475--567535	32	1.9	32	83	6	79	9	18	42	29	1.82
567445--567544	50	2.0	51	83	13	127	10	21	40	29	1.85
568198--568258	23	2.6	24	77	17	65	19	1	3	75	1.03
569871--569916	21	2.2	20	82	14	58	21	15	19	43	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
573290--573470	52	3.5	52	93	0	299	29	17	17	35	1.93
573479--573503	13	1.9	13	100	0	50	36	16	16	32	1.90
573546--573597	19	2.7	19	93	0	95	40	17	11	30	1.85
574309--574646	48	6.9	49	82	4	369	31	17	26	24	1.97
574357--574646	149	2.0	148	92	0	490	31	17	25	24	1.97
574666--574817	28	5.3	28	83	5	164	19	15	27	36	1.93
574692--575036	30	11.6	30	79	6	217	25	15	28	29	1.96
574814--574881	35	2.0	35	88	2	102	39	11	29	19	1.87
574867--575038	86	2.0	87	89	1	265	23	17	31	27	1.97
576181--576215	19	1.9	17	88	11	52	45	5	20	28	1.73
590314--590494	52	3.5	52	95	0	317	28	17	17	36	1.93
590503--590527	13	1.9	13	100	0	50	36	16	16	32	1.90
590570--590667	19	5.8	18	69	28	81	36	16	12	34	1.86
590565--590665	32	3.1	32	95	1	175	35	16	11	35	1.86
590589--590645	13	3.9	13	74	24	51	33	15	14	36	1.88
596286--596366	30	2.7	30	78	5	92	41	7	3	46	1.49
596993--597023	16	1.9	16	93	0	53	54	0	6	38	1.26
597087--597122	11	3.4	10	92	7	54	66	0	0	33	0.92
597173--597218	23	2.0	23	91	8	76	43	2	0	54	1.12
598108--598148	12	3.6	12	80	12	50	51	9	0	39	1.35
604444--604479	16	2.2	17	90	5	56	19	11	22	47	1.80
604774--604798	12	2.1	12	100	0	50	76	0	8	16	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
606146--606214	19	3.5	19	76	13	68	62	0	0	37	0.96
608187--608228	15	2.8	16	78	7	52	66	7	0	26	1.17
609324--609368	17	2.7	16	83	16	56	42	0	0	57	0.98
609317--609354	20	1.9	20	84	10	51	44	0	0	55	0.99
609329--609421	28	3.4	27	78	12	100	38	0	1	60	1.04
609340--609444	28	3.6	29	76	12	101	38	0	1	59	1.15
610647--610672	12	2.2	12	100	0	52	0	0	7	92	0.39
610990--611032	18	2.5	17	85	7	59	51	0	0	48	1.00
611411--611460	16	3.2	16	77	5	57	50	0	2	48	1.12
611420--611475	27	2.1	26	83	9	69	55	0	1	42	1.10

Tables:   1   2   3   4   5   6   7   8   9