genome.fa.s1.2.7.7.80.10.50.1000.42.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  42  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)
6857709--6857777	25	2.8	24	80	8	68	49	2	2	44	1.32
6857942--6858016	6	12.5	6	76	10	64	33	1	0	65	1.01
6857932--6858021	13	6.8	13	70	17	51	33	3	1	62	1.19
6859251--6859308	23	2.5	22	75	8	62	43	0	1	55	1.10
6859293--6859336	22	2.0	22	83	16	56	40	2	0	56	1.11
6859993--6860040	23	2.0	24	84	11	64	45	0	2	52	1.12
6860584--6860623	21	1.9	21	84	0	53	30	2	0	67	1.04
6860831--6860913	41	2.0	41	92	0	139	45	16	10	26	1.80
6860891--6860929	12	3.3	11	86	13	51	76	0	0	23	0.78
6865632--6865674	2	21.5	2	90	0	68	44	0	0	55	0.99
6866870--6866913	16	2.4	18	78	21	56	59	0	0	40	0.98
6866873--6866915	17	2.5	17	88	7	61	60	0	0	39	0.97
6870636--6871369	370	2.0	361	90	4	1150	38	10	7	43	1.68
6871949--6872012	33	1.9	33	96	0	119	35	6	6	51	1.52
6873004--6873059	24	2.7	20	77	20	60	57	0	0	42	0.99
6873400--6873448	6	8.0	6	86	4	62	59	0	0	40	0.98
6873401--6873475	25	3.0	26	86	7	95	52	0	0	48	1.00
6873440--6873515	38	2.0	38	85	10	102	44	0	2	52	1.14
6873597--6873633	15	2.4	17	82	17	53	43	0	2	54	1.14
6877518--6877613	46	2.1	46	92	3	158	45	8	6	39	1.59
6878751--6878817	32	2.1	32	83	5	82	56	8	10	23	1.61
6880846--6880882	2	18.5	2	100	0	74	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)
6881462--6881493	16	1.9	17	93	6	57	40	0	12	46	1.42
6882988--6883035	18	2.6	20	81	12	59	29	0	2	68	1.01
6883132--6883184	24	2.1	27	82	10	67	37	1	0	60	1.08
6884112--6884150	14	2.9	13	85	7	51	64	7	0	28	1.21
6885168--6885198	2	15.5	2	93	0	53	48	3	0	48	1.17
6885731--6885810	39	2.1	37	90	6	126	32	5	8	53	1.53
6886958--6886992	18	1.9	18	94	0	61	51	0	0	48	1.00
6886954--6886985	13	2.3	15	89	10	50	50	0	0	50	1.00
6887921--6887958	19	2.0	20	85	15	53	57	0	0	42	0.98
6890861--6890910	25	2.0	25	100	0	100	28	16	24	32	1.96
6894323--6894349	2	13.5	2	100	0	54	51	0	0	48	1.00
6900591--6900625	15	2.3	16	85	14	56	40	0	0	60	0.97
6900664--6900713	14	3.1	18	75	19	56	38	0	0	62	0.96
6900705--6900755	21	2.4	22	81	15	63	58	3	0	37	1.16
6900813--6900864	17	3.0	18	81	13	65	34	0	0	65	0.93
6901155--6901185	15	2.1	15	93	0	53	35	0	0	64	0.94
6901236--6901269	14	2.4	14	85	0	50	58	0	0	41	0.98
6901227--6901277	22	2.3	23	83	12	63	52	0	0	47	1.00
6901750--6901778	14	2.0	15	93	6	51	68	0	0	31	0.89
6902544--6902668	21	5.8	21	71	16	71	38	3	0	58	1.14
6902613--6902675	33	1.9	33	87	6	92	38	3	0	58	1.14
6902626--6902676	15	3.6	14	79	10	59	41	1	0	56	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6908795--6908828	2	17.0	2	93	0	59	47	0	0	52	1.00
6908903--6908950	15	3.1	15	82	14	53	62	0	2	35	1.07
6909982--6910026	2	22.5	2	95	0	81	48	2	0	48	1.13
6910228--6910268	19	2.1	20	82	13	50	46	0	2	51	1.14
6910870--6910904	2	17.5	2	100	0	70	51	0	0	48	1.00
6913485--6913599	58	2.0	57	96	1	212	33	22	6	38	1.79
6916103--6916173	3	23.0	3	80	11	72	28	0	4	67	1.09
6916803--6916858	25	2.3	23	79	11	60	58	0	0	41	0.98
6916809--6916859	25	2.1	26	82	17	65	62	0	0	37	0.95
6922973--6923008	17	2.2	17	90	9	58	63	0	0	36	0.94
6923803--6923855	25	2.1	25	100	0	106	39	18	18	22	1.92
6923973--6924038	16	4.2	16	69	21	50	62	0	1	36	1.05
6924528--6924575	25	1.9	25	82	0	60	52	0	0	47	1.00
6925078--6925121	22	2.0	22	86	4	63	31	4	2	61	1.28
6925562--6925621	30	2.0	29	87	9	86	60	0	0	40	0.97
6925563--6925620	15	3.9	15	74	17	66	62	0	0	37	0.96
6929551--6929634	41	2.0	41	100	0	168	39	2	9	48	1.49
6929612--6929650	2	19.5	2	100	0	78	51	0	0	48	1.00
6931680--6931741	30	2.1	31	84	6	83	35	11	3	50	1.55
6932189--6932225	18	2.1	18	90	10	58	21	45	0	32	1.52
6934753--6934817	12	5.4	12	75	3	51	56	0	0	43	0.99
6935261--6935301	3	13.7	3	100	0	82	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6936633--6936693	30	2.0	30	87	6	88	45	0	0	54	1.00
6937967--6938011	15	2.9	15	83	3	54	51	2	0	46	1.13
6939922--6939955	17	1.9	18	94	5	61	17	26	20	35	1.95
6941226--6941270	22	2.0	22	95	0	81	37	20	20	22	1.94
6941764--6941812	3	16.0	3	78	4	53	36	2	2	59	1.21
6947905--6947929	13	1.9	13	100	0	50	48	8	0	44	1.32
6950991--6951089	32	2.9	32	76	19	94	39	3	1	56	1.21
6951038--6951089	17	3.1	16	73	13	52	34	3	0	61	1.14
6950976--6951090	33	3.3	32	74	22	92	39	3	1	55	1.27
6951594--6951625	14	2.3	14	100	0	64	43	0	6	50	1.27
6951638--6951728	33	2.8	32	81	9	103	54	2	2	40	1.24
6951676--6951729	17	3.3	17	69	25	53	57	0	1	40	1.09
6952026--6952075	24	2.0	24	84	11	64	62	0	0	38	0.96
6953467--6953551	32	2.5	33	84	9	109	40	3	3	52	1.36
6958877--6958954	27	2.9	27	76	0	84	26	7	19	46	1.77
6959478--6959541	30	2.1	30	82	5	76	18	34	35	10	1.86
6960098--6960141	2	22.0	2	100	0	88	50	0	0	50	1.00
6960473--6960517	14	3.2	13	84	12	54	68	0	0	31	0.89
6960614--6960684	30	2.4	30	82	15	78	25	0	1	73	0.92
6960614--6960681	31	2.2	30	82	12	77	23	0	1	75	0.89
6962474--6962499	2	13.0	2	100	0	52	50	0	0	50	1.00
6962972--6963042	30	2.4	30	82	15	78	25	0	1	73	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6962972--6963039	31	2.2	30	82	12	77	23	0	1	75	0.89
6964830--6964870	2	21.0	2	85	5	57	48	0	2	48	1.14
6965228--6965307	37	2.1	39	86	6	110	51	0	0	48	1.00
6967369--6967407	10	4.2	9	87	12	53	33	0	0	66	0.92
6967369--6967415	17	2.7	18	83	6	62	36	0	0	63	0.94
6967327--6967407	27	2.9	28	80	7	103	35	2	1	60	1.18
6970092--6970122	15	2.0	16	93	6	55	3	6	0	90	0.55
6970091--6970127	9	4.4	9	86	13	53	8	8	0	83	0.80
6971704--6971760	23	2.4	25	80	11	66	45	5	0	49	1.24
6973957--6974005	18	2.7	18	83	0	62	38	24	22	14	1.91
6977529--6977580	2	26.0	2	92	0	86	46	0	3	50	1.20
6978315--6978347	2	16.5	2	100	0	66	48	0	0	51	1.00
6978854--6978900	12	3.7	13	81	10	53	53	0	0	46	1.00
6980165--6980206	17	2.3	18	80	19	52	45	0	0	54	0.99
6983265--6983308	16	2.8	16	80	13	54	0	22	0	77	0.77
6983269--6983306	19	2.0	20	94	5	69	0	21	0	78	0.74
6986185--6986223	14	2.8	14	84	11	53	38	0	0	61	0.96
6986280--6986314	14	2.4	15	90	4	54	22	0	0	77	0.78
6986278--6986322	16	2.9	15	84	15	65	22	0	0	77	0.76
6986976--6987032	18	3.3	16	79	15	60	40	0	1	57	1.09
6990148--6990187	12	3.3	12	89	0	62	0	12	0	87	0.54
6990148--6990184	16	2.4	16	95	4	67	0	10	0	89	0.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6990926--6990958	15	2.1	16	94	5	59	42	9	6	42	1.61
6991123--6991147	13	1.9	13	100	0	50	32	0	12	56	1.36
6993030--6993082	23	2.2	24	83	6	63	62	0	0	37	0.96
6993724--6993753	2	15.0	2	100	0	60	50	0	0	50	1.00
6996642--6996795	31	5.0	31	75	6	123	31	20	18	30	1.96
6996642--6996795	62	2.5	62	80	6	161	31	20	18	30	1.96
6997630--6997661	15	2.1	16	88	11	50	53	6	0	40	1.26
6999149--6999195	2	23.5	2	95	0	85	53	0	0	46	1.00
6999490--6999524	18	1.9	18	94	0	61	28	0	0	71	0.86
6999608--6999640	17	1.9	17	100	0	66	36	0	3	60	1.12

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