genome.fa.s3.2.7.7.80.10.50.1000.22.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  22  of  32  ( 3795 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)
3668939--3668999	16	3.6	16	78	8	68	49	1	0	49	1.10
3669192--3669225	13	2.5	14	85	9	52	32	0	0	67	0.91
3676150--3676180	4	7.8	4	92	0	53	74	0	25	0	0.82
3679120--3679156	2	18.5	2	100	0	74	48	0	51	0	1.00
3681836--3681864	2	14.5	2	100	0	58	48	0	0	51	1.00
3682650--3682708	19	3.1	18	76	16	57	45	0	1	52	1.10
3682895--3682930	14	2.4	16	81	18	58	16	11	16	55	1.68
3682832--3682990	79	2.0	79	100	0	318	12	18	17	50	1.77
3682911--3683031	65	1.9	64	92	1	206	11	22	17	48	1.79
3688929--3688972	18	2.4	18	84	0	52	38	0	9	52	1.33
3690914--3690946	2	16.5	2	100	0	66	48	0	0	51	1.00
3695722--3695746	3	8.3	3	100	0	50	0	36	0	64	0.94
3706036--3706068	2	16.5	2	100	0	66	51	0	0	48	1.00
3706866--3706943	38	2.1	38	90	4	122	28	1	24	46	1.61
3721250--3721308	29	2.1	29	87	3	84	49	0	11	38	1.40
3723773--3723827	14	3.9	14	77	15	51	32	0	0	67	0.91
3723772--3723836	22	3.0	22	78	14	73	32	0	1	66	1.01
3723768--3723836	35	1.9	35	88	8	104	31	0	1	66	1.00
3723767--3723827	12	4.5	13	74	20	54	32	0	0	67	0.91
3723909--3723954	7	6.6	7	78	16	51	45	2	0	52	1.13
3726944--3726993	26	1.9	26	88	8	75	66	0	0	34	0.92
3729844--3729878	2	17.5	2	88	11	54	45	0	2	51	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3730718--3730743	2	13.0	2	100	0	52	50	0	0	50	1.00
3736426--3736465	20	2.0	20	85	9	55	30	0	0	70	0.88
3736580--3736635	16	3.2	16	79	18	67	44	0	0	55	0.99
3736580--3736627	20	2.7	18	87	12	64	45	0	0	54	0.99
3736580--3736637	20	3.1	19	77	22	61	44	0	0	55	0.99
3736709--3736742	3	11.3	3	100	0	68	67	0	0	32	0.91
3737325--3737383	31	1.9	31	86	13	86	54	0	1	44	1.10
3738093--3738119	2	13.5	2	100	0	54	0	48	0	51	1.00
3739259--3739302	2	22.0	2	100	0	88	50	0	0	50	1.00
3742698--3742722	13	1.9	13	100	0	50	0	24	0	76	0.80
3745053--3745094	21	2.0	21	81	9	50	35	4	4	54	1.42
3751713--3751747	2	17.5	2	100	0	70	48	0	0	51	1.00
3752698--3752756	28	2.1	28	81	15	68	37	0	5	57	1.21
3752707--3752788	38	2.1	41	81	6	98	37	0	2	59	1.11
3755778--3755813	2	18.0	2	91	0	54	52	2	44	0	1.15
3758216--3758287	23	3.2	23	78	2	65	50	2	2	44	1.31
3758962--3759035	32	2.4	32	82	6	91	45	0	1	52	1.09
3759004--3759050	24	2.0	24	87	8	69	48	0	0	51	1.00
3764416--3764486	29	2.4	30	88	6	101	42	0	5	52	1.25
3764482--3764523	22	1.9	22	85	0	57	47	0	0	52	1.00
3765106--3765149	16	2.8	16	82	3	54	36	0	0	63	0.95
3765100--3765151	23	2.2	24	83	12	65	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3766693--3766730	20	1.9	20	88	0	58	52	0	2	44	1.14
3767016--3767055	2	20.5	2	94	5	73	47	0	0	52	1.00
3767281--3767306	2	13.0	2	100	0	52	50	0	0	50	1.00
3770668--3770750	20	4.0	20	72	14	62	51	1	1	45	1.16
3770668--3770727	18	3.2	18	73	13	59	51	0	0	48	1.00
3777024--3777057	16	2.1	16	100	0	68	44	11	11	32	1.77
3781290--3781331	18	2.3	19	88	8	61	45	0	0	54	0.99
3781307--3781349	16	2.6	18	82	14	56	44	0	0	55	0.99
3784288--3784328	21	1.9	22	90	5	66	43	0	0	56	0.99
3787162--3787200	21	1.9	20	89	5	60	33	2	5	58	1.33
3787604--3787639	13	2.5	15	86	13	58	41	0	0	58	0.98
3787604--3787660	29	2.0	28	82	3	69	38	0	1	59	1.08
3787595--3787651	16	3.9	15	76	21	50	40	0	0	59	0.97
3790597--3790626	14	2.2	14	94	5	53	53	0	0	46	1.00
3790957--3791019	15	4.5	14	68	20	51	60	1	3	34	1.22
3791443--3791592	34	4.4	34	88	0	221	26	8	26	38	1.85
3796003--3796153	34	4.5	34	88	0	223	25	7	27	39	1.84
3797459--3797488	2	15.0	2	100	0	60	50	0	0	50	1.00
3797646--3797684	2	19.5	2	100	0	78	51	0	0	48	1.00
3801028--3801060	2	16.5	2	100	0	66	51	0	0	48	1.00
3802145--3802210	33	2.0	34	82	8	82	53	1	1	43	1.19
3802136--3802218	20	4.1	20	68	14	53	53	1	1	44	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3802543--3802602	24	2.5	25	76	12	63	50	0	1	48	1.11
3802644--3802712	23	2.9	23	76	17	70	46	0	0	53	1.00
3806365--3806399	16	2.1	17	94	5	63	40	0	0	60	0.97
3806464--3806514	23	2.2	24	85	3	68	45	0	0	54	0.99
3806997--3807037	21	2.1	19	86	9	55	56	0	0	43	0.99
3807007--3807055	18	2.8	18	76	14	57	59	2	0	38	1.09
3809037--3809083	19	2.5	18	80	10	58	65	0	0	34	0.93
3809047--3809087	19	2.2	19	90	0	64	65	0	0	34	0.93
3817108--3817146	20	1.9	21	94	5	71	69	0	0	30	0.89
3824068--3824118	24	2.1	24	85	3	66	58	0	0	41	0.98
3824071--3824113	19	2.4	18	85	14	54	60	0	0	39	0.97
3824079--3824134	24	2.2	26	87	9	80	60	1	0	37	1.07
3824082--3824158	28	2.8	28	78	13	79	63	1	0	35	1.03
3824104--3824161	20	3.0	20	75	17	59	62	1	0	36	1.06
3831122--3831160	16	2.4	17	86	4	53	51	0	5	43	1.24
3831154--3831196	19	2.3	19	91	0	68	48	0	0	51	1.00
3831151--3831191	21	2.0	20	90	4	64	46	0	0	53	1.00
3835426--3835472	25	2.0	25	87	8	71	31	8	4	55	1.49
3837561--3837600	18	2.2	18	86	8	55	55	0	0	45	0.99
3837780--3837813	10	3.6	10	88	11	54	70	0	0	29	0.87
3837798--3837865	32	2.1	32	86	10	95	54	2	1	41	1.24
3839897--3839921	13	1.9	13	100	0	50	36	16	16	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3839982--3840006	13	1.9	13	100	0	50	32	16	16	36	1.90
3840015--3840143	52	2.5	52	94	0	222	34	17	17	30	1.94
3843282--3843365	21	4.0	21	75	3	71	48	5	5	39	1.52
3843370--3843466	21	4.4	22	78	16	112	49	6	4	40	1.47
3843626--3843706	42	2.0	41	87	2	117	50	7	3	38	1.48
3843588--3843704	21	5.7	21	75	9	89	52	9	3	35	1.51
3844249--3844279	13	2.4	13	94	0	53	29	0	3	67	1.06
3845089--3845148	22	2.5	24	86	7	79	56	0	0	43	0.99
3845076--3845157	22	3.6	22	80	13	78	56	0	0	43	0.99
3849199--3849231	3	11.0	3	100	0	66	66	0	0	33	0.92
3850121--3850159	15	2.6	15	84	8	53	43	0	7	48	1.31
3850185--3850294	14	7.5	15	70	26	76	52	0	0	47	1.00
3850147--3850294	75	2.0	74	80	12	169	52	0	1	45	1.09
3850179--3850310	27	4.9	27	69	18	87	53	0	0	46	1.00
3850203--3850306	45	2.2	49	81	16	130	53	0	0	46	1.00
3850209--3850310	54	1.9	52	82	7	125	53	0	0	46	1.00
3850209--3850302	15	5.8	18	68	27	68	54	0	0	45	0.99
3856599--3856626	6	4.7	6	100	0	56	50	0	0	50	1.00
3857281--3857314	17	1.9	18	88	5	52	61	0	0	38	0.96
3857933--3857990	30	2.0	29	86	3	80	65	3	0	31	1.09
3858572--3858638	4	16.8	4	79	14	50	77	1	20	0	0.85
3858560--3858630	17	4.2	16	76	16	63	77	1	21	0	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3858572--3858637	14	4.7	14	78	12	64	78	1	19	0	0.82
3858579--3858628	16	3.1	16	80	11	57	82	2	16	0	0.77
3858560--3858638	13	6.5	13	74	14	62	75	1	22	0	0.87
3858685--3858745	11	5.5	11	74	14	54	39	1	0	59	1.08
3858693--3858748	24	2.3	24	87	0	85	39	1	0	58	1.08
3858704--3858804	11	9.2	11	73	10	73	28	1	1	67	1.13
3858715--3858786	20	3.6	19	78	10	72	27	1	1	69	1.05
3858704--3858804	31	3.1	33	82	8	107	28	1	1	67	1.13
3859222--3859261	20	2.0	21	90	5	64	27	0	2	70	1.01
3860010--3860041	2	16.0	2	100	0	64	50	0	0	50	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