genome.fa.s4.2.7.7.80.10.50.1000.14.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  14  of  31  ( 3628 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)
3184039--3184081	21	2.2	20	91	8	70	55	4	4	34	1.41
3186268--3186299	15	2.1	16	94	5	57	62	0	0	37	0.95
3186268--3186299	8	4.1	8	92	8	57	62	0	0	37	0.95
3188311--3188344	16	2.1	17	94	5	61	67	0	5	26	1.13
3188317--3188351	16	2.2	16	89	0	52	77	0	5	17	0.96
3206252--3206292	21	2.0	22	85	9	59	19	9	9	60	1.55
3213355--3213384	3	10.0	3	100	0	60	66	0	33	0	0.92
3213506--3213548	2	22.0	2	90	4	70	0	48	0	51	1.00
3219970--3220024	27	2.0	27	82	0	65	61	5	1	30	1.29
3221175--3221203	2	14.5	2	100	0	58	51	0	0	48	1.00
3221480--3221513	18	1.9	18	94	5	61	41	0	0	58	0.98
3221508--3221543	17	2.2	16	90	5	54	47	0	0	52	1.00
3235097--3235122	3	8.7	3	100	0	52	34	34	30	0	1.58
3236335--3236397	30	2.1	31	90	3	101	50	0	0	49	1.00
3236461--3236501	21	1.9	22	85	5	57	46	4	0	48	1.23
3236487--3236530	14	3.0	15	80	6	54	59	0	0	40	0.98
3236559--3236587	3	9.7	3	100	0	58	68	0	0	31	0.89
3245007--3245057	17	2.9	17	72	13	50	68	0	0	31	0.90
3248537--3248567	2	15.5	2	100	0	62	48	0	0	51	1.00
3248934--3248958	3	8.3	3	100	0	50	64	0	0	36	0.94
3250005--3250058	7	7.7	7	95	0	81	37	33	0	29	1.58
3250324--3250348	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3250398--3250435	17	2.2	17	86	9	51	60	0	2	36	1.11
3250777--3250804	2	14.0	2	100	0	56	50	0	0	50	1.00
3251612--3251697	28	3.4	23	67	22	57	61	1	1	36	1.11
3256977--3257005	2	14.5	2	100	0	58	0	48	0	51	1.00
3260087--3260121	3	11.7	3	100	0	70	65	0	0	34	0.93
3263968--3264218	87	2.9	88	85	3	335	43	19	9	28	1.81
3265652--3265717	29	2.3	29	82	12	82	51	0	3	45	1.16
3267829--3267899	33	2.2	33	84	0	88	53	18	2	25	1.58
3271004--3271049	22	2.1	22	100	0	92	30	13	32	23	1.93
3284424--3284461	7	5.3	7	82	17	51	44	2	0	52	1.14
3284677--3284706	6	5.2	6	96	4	53	13	0	16	70	1.18
3285769--3285811	20	2.2	20	91	0	68	18	16	37	27	1.92
3288629--3288672	22	2.0	22	82	8	54	40	0	0	59	0.98
3289112--3289150	18	2.1	19	85	4	53	58	2	2	35	1.25
3289218--3289254	12	3.2	12	88	3	58	56	5	2	35	1.36
3289717--3289742	13	2.0	13	100	0	52	46	0	7	46	1.31
3295667--3295724	24	2.3	24	85	5	71	36	25	12	25	1.91
3295714--3295779	27	2.4	27	87	0	87	25	10	18	45	1.81
3295883--3295978	48	2.0	48	97	0	183	21	22	7	47	1.75
3296650--3296676	2	13.5	2	100	0	54	51	0	48	0	1.00
3298128--3298161	2	17.0	2	100	0	68	50	0	0	50	1.00
3299898--3299936	2	20.0	2	94	5	71	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3302920--3302986	35	1.9	35	85	11	93	46	0	0	53	1.00
3304083--3304110	2	14.0	2	100	0	56	50	0	0	50	1.00
3309983--3310029	21	2.2	21	100	0	94	65	8	8	17	1.44
3310948--3311022	20	3.8	20	78	3	71	40	10	13	36	1.79
3310945--3311022	40	2.0	39	84	2	102	39	11	12	35	1.80
3311680--3311734	27	2.0	27	96	0	101	43	16	0	40	1.48
3312406--3312488	29	2.9	29	77	12	73	59	3	0	37	1.15
3329668--3329705	15	2.4	16	83	16	53	55	0	2	42	1.14
3329717--3329757	17	2.4	17	88	8	57	48	0	2	48	1.14
3329726--3329761	17	2.2	17	95	5	65	50	0	2	47	1.15
3330183--3330226	20	2.1	21	87	4	63	36	0	0	63	0.95
3330178--3330255	34	2.3	33	82	10	88	38	0	0	61	0.96
3333886--3334071	69	2.7	70	94	2	315	40	15	11	33	1.82
3340000--3340133	68	2.0	67	88	1	196	22	19	19	38	1.93
3341331--3341376	23	2.2	22	78	17	53	30	2	4	63	1.26
3341439--3341476	19	2.1	19	90	5	60	68	0	0	31	0.90
3342348--3342382	2	17.5	2	87	0	52	45	2	2	48	1.32
3343205--3343246	19	2.3	19	91	4	68	30	0	2	66	1.04
3343805--3343863	30	2.1	27	84	9	73	54	0	0	45	0.99
3513680--3513706	14	1.9	14	100	0	54	0	14	0	85	0.61
3517528--3517553	2	13.0	2	100	0	52	50	0	0	50	1.00
3518923--3518955	11	3.0	11	95	0	57	30	9	9	51	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3520802--3520846	23	2.0	22	83	12	56	35	0	0	64	0.94
3520918--3520968	14	3.8	13	78	14	50	35	0	1	62	1.06
3520924--3520969	14	3.3	14	77	17	51	30	0	2	67	1.03
3522329--3522358	4	7.8	4	92	7	53	23	0	0	76	0.78
3522836--3522898	10	6.6	10	71	23	55	39	0	0	60	0.97
3522837--3522902	16	4.2	16	90	9	109	39	0	0	60	0.97
3522838--3522898	30	2.0	31	96	3	115	37	0	0	62	0.96
3522929--3522959	16	1.9	16	93	0	53	38	0	0	61	0.96
3523314--3523497	94	2.0	93	93	1	314	32	16	22	28	1.96
3523666--3523720	20	2.8	19	78	15	58	45	0	3	50	1.19
3523772--3523806	2	17.5	2	100	0	70	51	0	0	48	1.00
3526416--3526489	12	6.5	11	75	16	71	5	16	1	77	1.03
3526444--3526488	6	7.7	6	85	5	65	0	15	2	82	0.77
3526416--3526498	34	2.5	33	84	4	94	4	18	1	75	1.04
3529432--3529460	2	14.5	2	100	0	58	48	0	0	51	1.00
3532371--3532412	16	2.6	16	84	3	57	42	0	2	54	1.13
3533428--3533472	21	2.1	21	88	8	65	48	8	4	37	1.55
3534012--3534063	2	26.0	2	100	0	104	50	0	0	50	1.00
3536033--3536093	10	5.9	11	75	21	53	72	0	0	27	0.85
3536027--3536112	22	3.7	23	78	15	79	66	0	1	32	1.00
3536021--3536097	17	4.8	16	73	12	68	68	0	0	31	0.90
3536020--3536172	28	5.3	29	71	15	104	59	0	0	39	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3537333--3537391	30	2.0	30	83	6	75	55	1	0	42	1.09
3538060--3538092	16	2.1	16	88	11	50	42	0	0	57	0.98
3538066--3538129	32	2.0	33	84	9	87	46	1	0	51	1.10
3540142--3540171	2	15.0	2	100	0	60	50	0	50	0	1.00
3545561--3545588	2	14.0	2	100	0	56	0	50	0	50	1.00
3553583--3553620	15	2.5	15	91	4	58	36	0	0	63	0.95
3554478--3554523	23	2.0	23	83	8	58	47	6	23	21	1.74
3558100--3558128	2	14.5	2	100	0	58	51	0	0	48	1.00
3561987--3562034	21	2.2	21	85	3	60	58	0	0	41	0.98
3561998--3562059	21	2.9	21	81	11	72	53	0	0	46	1.00
3562232--3562260	2	14.5	2	100	0	58	0	48	0	51	1.00
3568350--3568380	12	2.6	12	89	0	53	29	45	9	16	1.79
3569351--3569382	15	2.1	16	88	11	50	59	0	0	40	0.97
3571551--3571598	13	3.7	13	74	0	51	37	4	4	54	1.39
3571552--3571601	26	1.9	26	87	0	73	36	6	4	54	1.44
3578456--3578499	3	14.7	3	95	0	79	65	0	2	31	1.05
3579768--3579807	19	2.1	19	100	0	80	32	17	20	30	1.95
3587495--3587529	2	17.5	2	100	0	70	0	48	0	51	1.00
3589564--3589603	17	2.3	17	86	4	53	50	0	0	50	1.00
3589634--3589672	17	2.2	17	86	9	51	61	2	0	35	1.10
3592038--3592133	45	2.1	45	98	1	183	32	17	15	34	1.92
3593846--3593927	40	2.0	40	97	0	155	35	8	17	39	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3594434--3594465	2	16.0	2	100	0	64	50	0	0	50	1.00
3596794--3596861	28	2.3	30	78	12	79	41	4	0	54	1.20
3597154--3597207	22	2.4	21	82	14	63	33	1	0	64	1.04
3597152--3597206	21	2.5	23	83	13	71	36	1	0	61	1.06
3597793--3597839	16	2.9	16	76	14	51	44	2	0	53	1.12
3599328--3599401	33	2.3	32	77	15	80	40	6	0	52	1.28
3599873--3599916	18	2.6	17	78	7	54	47	0	11	40	1.39
3600072--3600107	14	2.6	14	86	0	54	80	0	2	16	0.83
3604527--3604554	2	14.0	2	100	0	56	50	0	0	50	1.00
3608280--3608308	2	14.5	2	100	0	58	0	48	0	51	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