genome.fa.s1.2.7.7.80.10.50.1000.45.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  45  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)
7268985--7269049	30	2.2	29	79	15	71	60	0	0	40	0.97
7269193--7269238	22	2.1	21	84	11	58	45	6	0	47	1.28
7269322--7269366	18	2.5	18	80	20	58	66	2	0	31	1.04
7269363--7269420	22	2.7	20	84	10	62	39	3	0	56	1.16
7270007--7270054	22	2.2	22	85	3	62	27	0	0	72	0.84
7270005--7270056	16	3.1	18	78	15	67	32	0	0	67	0.91
7270024--7270062	18	2.2	17	86	4	51	35	0	0	64	0.94
7270099--7270136	18	2.1	19	85	5	51	52	0	0	47	1.00
7272542--7272570	15	1.9	15	100	0	58	41	0	0	58	0.98
7272520--7272681	84	1.9	84	91	0	261	52	2	3	41	1.30
7272956--7272989	2	17.0	2	100	0	68	50	0	0	50	1.00
7273154--7273192	2	19.5	2	100	0	78	48	0	0	51	1.00
7272873--7273269	203	2.0	201	91	3	654	36	19	14	29	1.91
7275536--7275617	30	2.7	30	85	7	96	53	0	0	46	1.00
7275547--7275634	47	1.9	45	84	9	115	52	0	0	47	1.00
7276551--7276575	1	25.0	1	100	0	50	0	0	100	0	0.00
7279299--7279325	13	2.1	13	100	0	54	37	7	14	40	1.74
7282860--7282912	2	26.5	2	100	0	106	50	0	0	49	1.00
7283052--7283111	24	2.5	22	77	15	57	46	1	1	50	1.21
7285162--7285194	15	2.2	15	89	10	50	54	3	3	39	1.31
7288480--7288512	17	1.9	17	93	0	57	39	0	0	60	0.97
7289500--7289557	22	3.2	17	76	23	64	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7289519--7289595	32	2.3	34	82	10	88	44	1	0	54	1.08
7289500--7289564	5	13.6	5	75	18	59	41	0	0	58	0.98
7290102--7290132	2	15.5	2	100	0	62	51	0	0	48	1.00
7291417--7291471	25	2.2	26	80	9	60	61	0	1	36	1.06
7292889--7292954	28	2.4	27	80	11	82	43	0	0	56	0.99
7292905--7292955	15	3.6	14	76	12	50	49	0	0	50	1.00
7292910--7293010	51	2.0	51	81	11	118	50	0	0	47	1.14
7293214--7293247	14	2.4	14	90	0	59	82	0	17	0	0.67
7293206--7293245	21	1.9	21	90	10	64	85	0	12	2	0.71
7298389--7298437	22	2.2	22	82	17	66	53	0	0	46	1.00
7298351--7298423	32	2.6	25	72	25	65	53	0	0	46	1.00
7298572--7298598	11	2.5	11	100	0	54	25	0	0	74	0.83
7299673--7299706	12	2.8	12	86	4	50	79	0	11	8	0.94
7300193--7300255	28	2.3	28	83	2	74	46	4	0	49	1.23
7316594--7316636	22	1.9	23	85	4	61	41	2	2	53	1.26
7317191--7317224	2	17.0	2	100	0	68	50	0	0	50	1.00
7324997--7325021	4	6.2	4	100	0	50	76	0	0	24	0.80
7325260--7325295	2	18.0	2	100	0	72	50	0	0	50	1.00
7325544--7325610	26	2.4	27	80	14	75	55	0	1	43	1.09
7325748--7325787	2	20.0	2	100	0	80	50	0	0	50	1.00
7325977--7326010	7	4.7	7	88	3	50	55	2	0	41	1.15
7327133--7327236	14	7.6	14	68	23	53	60	0	1	37	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7327182--7327243	27	2.1	31	85	11	87	56	0	0	43	0.99
7327195--7327253	8	7.6	8	78	14	61	57	0	1	40	1.09
7327465--7327693	75	3.0	75	85	5	291	31	17	14	36	1.90
7329441--7329497	21	2.6	22	73	15	64	40	0	0	59	0.97
7330828--7330911	17	4.9	17	68	13	57	54	3	0	41	1.17
7331398--7331443	3	15.3	3	100	0	92	32	0	0	67	0.91
7331627--7331659	2	16.5	2	100	0	66	51	0	0	48	1.00
7331769--7331817	16	3.1	15	82	14	55	51	2	0	46	1.12
7331786--7331862	40	1.9	41	81	7	95	53	3	0	42	1.19
7331892--7331920	2	14.5	2	100	0	58	51	0	0	48	1.00
7332245--7332277	11	2.8	12	90	9	50	57	0	0	42	0.98
7332245--7332282	13	3.1	13	88	7	53	60	0	0	39	0.97
7334023--7334065	14	3.1	14	76	3	52	53	0	0	46	1.00
7338086--7338151	32	2.1	32	97	0	123	37	12	0	50	1.40
7347793--7347843	21	2.4	21	81	12	59	33	0	0	66	0.92
7347887--7347941	22	2.5	22	80	17	60	30	0	1	67	1.01
7348237--7348289	22	2.4	21	75	9	52	45	0	1	52	1.11
7348252--7348311	28	2.1	29	85	11	81	46	0	1	51	1.10
7348953--7348995	17	2.4	18	84	3	52	60	0	2	37	1.10
7350866--7350913	19	2.5	19	75	0	51	14	20	0	64	1.28
7350951--7351000	23	2.1	24	85	3	66	52	4	8	36	1.50
7351205--7351268	31	2.1	29	82	5	74	59	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7351273--7351334	32	2.0	31	87	9	90	54	8	3	33	1.46
7351323--7351361	20	1.9	21	84	5	53	33	2	2	61	1.23
7352066--7352114	14	3.6	13	81	8	62	42	0	0	57	0.99
7352056--7352113	27	2.2	26	84	9	73	43	0	0	56	0.99
7352066--7352148	41	2.0	41	84	9	107	39	3	1	55	1.25
7353575--7353622	19	2.8	17	87	9	62	22	0	14	62	1.32
7360041--7360089	2	25.0	2	95	4	91	51	0	0	48	1.00
7365111--7365195	42	1.9	46	86	9	124	52	0	0	47	1.00
7368028--7368083	25	2.3	24	79	11	62	41	0	1	57	1.09
7368497--7368536	15	2.7	14	88	11	62	75	2	0	22	0.93
7370295--7370349	23	2.4	23	93	0	101	50	0	0	49	1.00
7372241--7372273	3	11.0	3	100	0	66	33	0	0	66	0.92
7373628--7373673	23	2.0	23	83	4	58	39	4	4	52	1.41
7374374--7374398	11	2.3	11	100	0	50	24	16	24	36	1.94
7377512--7377585	36	2.1	36	94	0	130	44	13	10	31	1.78
7377588--7377630	2	21.0	2	85	4	59	48	6	0	44	1.29
7378795--7378821	2	13.5	2	100	0	54	48	0	0	51	1.00
7381489--7381534	2	23.0	2	90	0	74	45	0	2	52	1.13
7381868--7381917	24	2.1	24	88	0	73	48	8	4	40	1.51
7383615--7383655	2	20.5	2	89	0	55	43	0	4	51	1.23
7384197--7384229	17	1.9	17	100	0	66	33	12	6	48	1.65
7386152--7386200	15	3.1	15	79	5	53	57	0	0	42	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7386171--7386229	23	2.6	24	79	15	72	52	0	0	47	1.00
7386796--7386835	14	2.8	14	82	17	55	42	0	0	57	0.98
7386803--7386828	7	3.7	7	100	0	52	42	0	0	57	0.98
7386834--7386867	17	1.9	18	88	5	52	35	8	2	52	1.47
7390794--7390844	26	2.0	26	84	7	68	43	0	1	54	1.11
7391475--7391546	22	3.3	22	71	9	67	38	5	0	55	1.23
7391518--7391577	25	2.4	26	81	8	72	33	1	0	65	1.03
7391903--7391963	31	1.9	32	90	3	97	47	0	0	52	1.00
7391904--7391978	31	2.5	31	82	6	91	49	0	0	50	1.00
7392594--7392646	17	3.0	17	86	5	61	41	0	0	58	0.98
7401065--7401101	2	18.5	2	100	0	74	48	0	0	51	1.00
7401594--7401645	17	3.2	16	82	15	54	44	0	0	55	0.99
7406825--7406874	24	2.0	25	81	11	59	58	0	0	42	0.98
7407455--7407492	16	2.4	16	86	8	51	39	10	0	50	1.37
7407767--7407822	16	3.6	16	79	18	73	69	0	0	30	0.89
7407781--7407826	21	2.1	22	84	4	58	71	0	0	28	0.86
7407848--7407899	18	2.7	19	75	22	54	53	0	0	46	1.00
7408995--7409024	4	7.5	4	92	0	51	23	0	3	73	0.98
7409345--7409372	2	14.0	2	100	0	56	50	0	0	50	1.00
7409791--7409853	15	4.0	15	84	10	81	57	0	1	41	1.08
7409767--7409854	6	15.3	6	69	23	57	53	0	1	45	1.07
7409768--7409855	5	16.6	5	71	19	63	54	0	1	44	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7411000--7411029	2	14.5	2	93	6	51	46	0	3	50	1.18
7412747--7412791	18	2.5	18	86	13	74	57	13	11	17	1.64
7412845--7412920	39	1.9	39	97	0	143	19	15	19	44	1.86
7413722--7413799	25	3.0	26	75	7	77	56	5	0	38	1.22
7414337--7414370	17	1.9	18	88	5	52	44	0	8	47	1.34
7415665--7415689	12	2.1	12	100	0	50	32	8	24	36	1.84
7416604--7416645	17	2.3	19	92	8	70	45	0	0	54	0.99
7416745--7416782	3	12.7	3	100	0	76	65	0	0	34	0.93
7418789--7418813	2	12.5	2	100	0	50	52	0	0	48	1.00
7419107--7419139	2	16.5	2	100	0	66	51	0	0	48	1.00

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