genome.fa.s1.2.7.7.80.10.50.1000.49.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  49  of  52  ( 6211 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)
7947703--7947737	18	1.9	18	94	0	61	45	0	0	54	0.99
7947724--7947776	21	2.7	20	74	11	56	43	0	1	54	1.11
7947769--7947801	16	2.0	17	88	5	50	42	0	0	57	0.98
7948304--7948360	27	2.1	27	84	12	73	33	0	3	63	1.12
7949400--7949454	6	9.0	6	81	15	51	47	0	0	52	1.00
7949575--7949653	21	3.9	19	73	12	59	51	1	0	46	1.08
7949719--7949777	22	2.6	23	79	10	68	54	3	0	42	1.17
7950010--7950055	15	3.3	15	76	14	53	39	0	0	60	0.97
7950003--7950055	13	4.0	13	79	13	54	43	0	0	56	0.99
7950200--7950233	8	4.1	8	88	7	50	23	0	5	70	1.09
7950271--7950341	33	2.1	35	84	7	94	45	1	2	50	1.25
7950333--7950392	22	2.8	21	75	10	59	40	1	0	58	1.08
7950417--7950565	34	4.3	35	68	18	123	41	0	1	56	1.12
7950715--7950767	18	2.9	18	75	13	54	43	0	0	56	0.99
7951635--7951692	6	9.7	6	78	0	53	53	0	37	8	1.32
7951628--7951698	15	4.7	15	82	0	88	50	1	36	11	1.47
7951650--7951699	18	2.8	18	84	0	55	50	0	40	10	1.36
7952227--7952264	2	19.0	2	100	0	76	50	0	50	0	1.00
7952853--7952897	16	2.6	18	80	19	60	42	0	0	57	0.98
7952863--7952923	25	2.3	26	81	13	72	40	0	1	57	1.08
7953859--7953899	21	2.0	21	90	9	66	58	0	0	41	0.98
7956445--7956507	30	2.1	30	90	0	99	55	1	3	39	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7956837--7956885	14	3.5	13	81	13	53	38	2	0	59	1.09
7956999--7957089	21	4.2	21	66	18	60	35	2	1	61	1.15
7957555--7957622	24	2.9	25	80	12	74	48	0	0	51	1.00
7957770--7957836	2	34.5	2	79	5	66	46	5	0	47	1.27
7958545--7958618	24	3.2	23	77	12	80	55	0	0	44	0.99
7958545--7958606	22	2.7	23	82	9	65	59	0	0	40	0.97
7958548--7958650	43	2.4	42	82	9	118	57	0	0	41	1.05
7959125--7959168	22	2.0	22	91	8	72	25	25	0	50	1.50
7959651--7959694	21	2.0	22	82	4	54	34	6	2	56	1.38
7959656--7959713	21	2.8	21	78	0	62	39	5	3	51	1.41
7959949--7959994	22	2.1	22	88	4	67	39	0	0	60	0.97
7961030--7961068	18	2.2	18	85	0	51	48	0	2	48	1.15
7961522--7961570	2	24.0	2	91	4	80	46	2	0	51	1.12
7962991--7963033	22	2.0	22	86	9	61	37	0	0	62	0.95
7963198--7963237	19	2.0	20	85	4	55	22	7	0	70	1.12
7964031--7964060	14	2.1	15	93	6	53	46	0	0	53	1.00
7965041--7965076	6	5.8	6	87	6	54	72	0	0	27	0.85
7965040--7965078	12	3.2	12	96	3	69	74	0	0	25	0.82
7965041--7965076	19	1.9	18	88	5	54	72	0	0	27	0.85
7965034--7965087	21	2.5	22	79	14	58	70	1	0	27	0.98
7965040--7965080	13	3.2	13	89	6	66	73	0	0	26	0.84
7965333--7965370	17	2.1	19	85	9	53	50	0	7	42	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7970713--7970743	2	15.5	2	100	0	62	0	48	0	51	1.00
7974628--7974682	22	2.5	22	79	8	58	50	0	0	49	1.00
7975055--7975237	34	5.4	34	88	0	260	25	7	27	40	1.81
7975055--7975237	102	1.8	101	92	1	312	25	7	27	40	1.81
7975542--7975604	19	3.3	19	90	0	90	28	17	19	34	1.94
7979670--7979854	34	5.5	34	89	0	273	25	7	27	40	1.82
7979670--7979854	102	1.8	101	94	1	325	25	7	27	40	1.82
7992413--7992516	53	1.9	54	88	1	156	47	7	25	19	1.76
7993530--7993599	33	2.1	33	81	7	79	44	2	0	52	1.15
7993604--7993703	28	3.6	28	71	10	71	59	4	1	36	1.23
7993768--7993842	25	3.0	25	70	16	66	58	0	0	41	0.98
7993797--7993833	16	2.2	17	90	4	58	62	0	0	37	0.96
7993803--7993845	21	2.0	22	86	9	61	58	0	0	41	0.98
7999523--7999584	27	2.2	28	77	2	72	51	0	0	48	1.00
7999525--7999584	21	3.0	21	78	9	63	51	0	0	48	1.00
8000504--8000539	15	2.4	15	90	9	56	36	5	5	52	1.48
8000692--8000743	19	2.5	22	81	12	65	38	1	1	57	1.21
8000783--8000835	21	2.4	23	78	6	65	54	1	1	41	1.22
8001652--8001711	27	2.2	28	91	8	97	63	0	5	31	1.16
8001657--8001718	28	2.2	28	88	5	90	64	1	4	29	1.23
8005112--8005162	13	3.8	15	66	28	51	45	0	0	54	0.99
8005422--8005449	2	14.0	2	100	0	56	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
8010619--8010672	25	2.2	25	83	6	65	57	0	5	37	1.22
8012293--8012341	7	6.1	8	82	17	50	40	0	0	59	0.98
8012293--8012336	15	2.9	15	78	21	56	43	0	0	56	0.99
8012533--8012583	24	2.2	22	86	6	66	68	0	3	27	1.07
8012578--8012629	21	2.4	21	84	9	61	53	0	0	46	1.00
8012569--8012643	32	2.3	33	83	4	89	54	0	0	45	0.99
8013357--8013405	22	2.1	24	88	7	75	67	0	0	32	0.91
8013373--8013457	37	2.3	37	80	12	93	60	0	0	40	0.97
8013403--8013442	20	2.0	21	85	14	57	60	0	0	40	0.97
8014596--8014652	17	3.5	15	80	9	51	64	1	0	33	1.04
8014596--8014646	23	2.2	22	83	13	59	66	0	0	33	0.92
8016731--8016787	20	2.9	20	84	2	71	28	0	3	68	1.06
8017327--8017359	13	2.4	14	90	10	50	3	21	0	75	0.93
8018162--8018226	32	2.0	31	82	11	78	46	0	1	52	1.10
8018196--8018236	20	2.0	21	90	4	66	51	0	2	46	1.14
8018715--8018760	24	1.9	24	86	0	65	32	6	17	43	1.75
8022672--8022732	30	2.0	30	96	0	113	26	13	18	42	1.86
8024121--8024199	40	2.0	40	80	9	92	49	7	7	35	1.60
8026731--8026802	25	2.9	25	80	12	69	61	0	4	34	1.16
8026759--8026787	14	2.0	15	93	6	51	62	0	0	37	0.96
8027008--8027061	2	27.0	2	100	0	108	50	0	0	50	1.00
8028107--8028137	2	15.5	2	100	0	62	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
8029262--8029293	15	2.1	15	100	0	64	34	31	0	34	1.58
8029447--8029515	22	3.0	23	78	14	79	55	0	0	44	0.99
8029469--8029538	33	2.1	34	82	12	83	54	1	0	44	1.09
8029796--8029847	16	3.3	16	81	2	61	59	1	1	36	1.19
8031553--8031579	4	6.8	4	100	0	54	77	0	22	0	0.76
8032319--8032343	3	8.3	3	100	0	50	36	32	0	32	1.58
8033784--8033835	2	27.0	2	88	7	81	51	1	0	46	1.12
8038920--8038956	19	1.9	19	89	10	58	43	0	2	54	1.14
8039902--8039934	15	2.1	17	88	11	52	51	0	3	45	1.16
8039955--8039998	17	2.7	16	82	6	52	50	0	0	50	1.00
8040847--8040924	22	3.8	21	76	10	63	50	1	0	48	1.09
8041756--8041797	16	2.6	16	81	14	50	45	0	0	54	0.99
8042387--8042425	18	2.2	19	86	9	55	51	7	0	41	1.31
8043305--8043336	5	6.6	5	92	7	57	18	0	0	81	0.70
8047234--8047272	6	6.5	6	96	0	69	61	0	0	38	0.96
8048851--8048892	22	1.9	22	90	9	68	61	0	0	38	0.96
8054286--8054318	16	2.1	16	94	0	57	60	3	0	36	1.12
8054316--8054368	9	5.4	10	73	13	56	33	0	0	66	0.92
8054316--8054364	19	2.6	18	87	6	62	30	0	0	69	0.89
8058832--8058892	29	2.1	29	82	8	72	52	0	1	45	1.10
8059080--8059126	2	23.5	2	95	0	85	2	46	0	51	1.13
8059488--8059531	11	3.8	12	85	8	56	29	0	0	70	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
8059526--8059559	17	1.9	18	88	5	52	52	0	0	47	1.00
8059905--8059961	24	2.4	23	75	18	62	43	1	0	54	1.10
8060396--8060428	16	2.1	16	88	11	50	27	0	0	72	0.85
8060536--8060603	26	2.5	28	74	6	70	50	1	1	47	1.19
8061139--8061234	13	7.5	13	74	13	76	40	1	2	56	1.18
8061230--8061284	22	2.5	21	80	8	65	61	0	0	38	0.96
8061302--8061352	23	2.2	23	82	0	57	52	7	0	39	1.30
8061345--8061428	19	4.4	18	76	18	73	71	3	0	25	1.02
8061438--8061539	32	3.2	31	75	15	84	44	4	0	50	1.23
8061443--8061548	31	3.5	31	79	12	89	46	3	0	50	1.19

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