genome.fa.s11.2.7.7.80.10.50.1000.21.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: Scaffold11
Parameters: 2 7 7 80 10 50 1000
Length:  5230303

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   

This is table  21  of  29  ( 3461 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)
3205701--3205825	39	3.2	39	62	10	101	32	3	8	56	1.45
3206178--3206211	18	1.9	17	88	5	50	41	0	2	55	1.15
3207254--3207316	26	2.4	25	81	5	72	49	1	0	49	1.10
3207273--3207328	26	2.2	25	81	9	60	51	1	1	44	1.22
3222215--3222258	2	22.0	2	90	0	70	47	2	0	50	1.13
3225119--3225147	2	15.0	2	92	7	51	48	0	0	51	1.00
3228591--3228623	2	17.0	2	93	6	59	51	0	0	48	1.00
3231752--3231788	13	2.8	13	87	0	56	21	24	37	16	1.93
3233114--3233140	6	4.5	6	100	0	54	14	0	48	37	1.45
3233705--3233750	2	23.5	2	91	4	76	50	2	0	47	1.13
3252183--3252207	2	12.5	2	100	0	50	0	48	0	52	1.00
3252207--3252238	2	15.5	2	93	6	55	46	0	3	50	1.17
3252514--3252568	28	1.9	29	85	10	78	54	0	0	45	0.99
3252703--3252751	15	3.1	17	77	14	59	44	4	2	48	1.33
3253506--3253537	2	16.0	2	100	0	64	50	0	0	50	1.00
3254414--3254465	21	2.5	20	75	12	50	44	1	0	53	1.11
3254669--3254701	2	16.5	2	100	0	66	51	0	0	48	1.00
3255087--3255129	2	22.5	2	88	9	63	46	0	0	53	1.00
3255418--3255469	21	2.4	23	78	15	67	55	5	0	38	1.24
3257346--3257404	22	2.7	21	76	7	64	64	3	3	28	1.26
3258127--3258161	18	1.9	18	88	0	52	74	5	0	20	1.02
3258181--3258231	3	17.3	3	95	4	95	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)
3259688--3259752	19	3.5	18	77	10	60	61	0	0	38	0.96
3259936--3259973	3	12.7	3	100	0	76	31	0	0	68	0.90
3262115--3262157	2	21.5	2	100	0	86	51	0	0	48	1.00
3262749--3262785	14	2.6	14	91	0	56	40	0	8	51	1.32
3262749--3262781	10	3.3	10	95	0	57	42	0	6	51	1.26
3263135--3263172	10	3.6	11	79	13	53	65	0	0	34	0.93
3263142--3263226	18	4.7	18	74	18	61	55	1	0	43	1.07
3263142--3263226	20	4.6	19	77	18	74	55	1	0	43	1.07
3263168--3263202	14	2.6	14	90	4	54	54	0	0	45	0.99
3263148--3263256	32	3.5	32	77	15	104	54	0	0	44	1.06
3263158--3263255	28	3.3	27	79	13	88	54	1	0	44	1.07
3263678--3263708	13	2.3	14	94	5	55	51	0	0	48	1.00
3265310--3265405	16	5.6	17	73	17	67	67	3	2	27	1.16
3265900--3265957	20	2.9	21	70	21	52	48	0	0	51	1.00
3265953--3265995	21	2.0	22	82	13	54	41	0	0	58	0.98
3265930--3266008	18	4.4	18	69	16	65	51	0	0	48	1.00
3265923--3266027	54	1.9	52	83	11	131	50	0	0	48	1.07
3267879--3267920	21	2.0	20	86	4	57	54	0	0	45	0.99
3268200--3268266	35	1.9	34	82	11	82	43	0	0	56	0.99
3268237--3268287	22	2.3	23	90	10	79	37	0	0	62	0.95
3269133--3269168	2	18.0	2	100	0	72	50	0	0	50	1.00
3269404--3269453	19	2.7	19	84	3	66	70	0	2	28	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3269417--3269449	13	2.6	13	90	4	50	69	0	0	30	0.88
3269405--3269479	8	9.6	8	76	12	50	68	0	1	30	0.98
3269428--3269482	4	13.5	4	79	9	58	67	0	0	32	0.91
3269527--3269563	16	2.2	17	86	13	51	0	16	16	67	1.23
3272865--3272923	18	3.5	17	73	20	52	37	1	0	61	1.07
3272852--3272923	32	2.1	34	85	12	96	41	1	0	56	1.07
3272908--3272949	13	3.4	13	81	18	54	38	0	0	61	0.96
3272908--3272953	24	1.9	24	86	8	67	36	0	0	63	0.95
3272850--3272951	17	5.6	18	67	30	58	41	0	0	57	1.05
3272871--3272956	30	3.0	30	71	21	85	39	1	0	59	1.05
3275728--3275764	18	2.1	18	90	10	58	37	0	0	62	0.96
3276387--3276432	11	3.8	12	80	16	51	36	0	0	63	0.95
3276376--3276436	30	2.0	30	84	6	79	34	1	0	63	1.04
3280582--3280619	2	19.0	2	100	0	76	50	0	50	0	1.00
3282218--3282243	2	13.0	2	100	0	52	50	0	0	50	1.00
3283341--3283501	49	3.2	48	80	5	178	36	18	15	30	1.92
3283341--3283501	50	3.2	49	81	3	180	36	18	15	30	1.92
3287875--3288046	50	3.5	50	82	1	211	35	18	15	31	1.91
3288178--3288211	6	5.7	6	100	0	68	32	17	0	50	1.47
3293701--3293737	20	2.0	20	84	10	51	48	8	0	43	1.32
3293815--3293857	20	2.2	20	86	0	59	32	0	0	67	0.91
3293870--3293931	21	3.0	21	77	11	74	35	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3293836--3293919	27	3.2	27	76	10	66	39	1	0	59	1.05
3298033--3298084	13	4.0	13	76	16	54	42	0	1	55	1.10
3298041--3298080	13	2.9	14	81	7	55	45	0	0	55	0.99
3298152--3298191	18	2.2	18	86	0	53	62	0	5	32	1.17
3300877--3300902	2	13.0	2	100	0	52	50	0	0	50	1.00
3301089--3301127	20	2.0	20	85	5	53	51	0	0	48	1.00
3306461--3306522	29	2.1	29	91	5	99	25	24	22	27	2.00
3310417--3310459	15	2.9	15	78	0	50	44	2	2	51	1.27
3321641--3321671	3	10.3	3	100	0	62	35	0	0	64	0.94
3322367--3322394	2	14.0	2	100	0	56	50	0	0	50	1.00
3325281--3325310	13	2.2	14	94	5	53	53	0	0	46	1.00
3325338--3325380	23	2.0	23	90	9	72	48	0	2	48	1.14
3325871--3325973	17	6.5	17	67	22	73	60	0	0	39	0.97
3325884--3325974	27	3.5	27	71	14	84	60	0	0	39	0.97
3325871--3325971	6	17.2	6	68	13	50	60	0	0	39	0.97
3327958--3327987	15	2.0	15	93	0	51	56	0	0	43	0.99
3334193--3334223	2	15.5	2	93	0	53	51	3	0	45	1.17
3342014--3342046	2	16.5	2	100	0	66	51	0	0	48	1.00
3342684--3342713	2	15.0	2	100	0	60	50	0	0	50	1.00
3348145--3348185	20	2.0	20	85	4	55	46	0	0	53	1.00
3350881--3350946	16	3.9	17	75	13	64	51	0	0	48	1.00
3350882--3350956	5	14.8	5	73	13	64	50	0	0	49	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3350882--3350948	35	1.9	35	87	6	100	50	0	0	49	1.00
3350898--3350956	15	4.3	15	81	18	74	49	0	0	50	1.00
3350879--3350962	26	3.3	26	80	11	93	47	1	0	51	1.08
3360382--3360410	2	14.5	2	100	0	58	0	48	0	51	1.00
3362229--3362261	2	16.5	2	100	0	66	0	48	0	51	1.00
3372515--3372539	6	4.2	6	100	0	50	84	0	0	16	0.63
3374231--3374273	22	1.9	22	86	13	61	39	0	0	60	0.97
3374805--3374844	2	20.0	2	100	0	80	50	0	0	50	1.00
3378005--3378057	20	2.7	20	76	5	54	67	5	0	26	1.12
3379768--3379820	21	2.6	21	79	11	56	45	0	3	50	1.19
3381730--3381762	2	16.5	2	100	0	66	48	0	0	51	1.00
3382320--3382352	2	17.0	2	87	6	50	51	3	0	45	1.16
3382686--3382723	2	19.0	2	100	0	76	50	0	0	50	1.00
3383104--3383273	83	2.0	83	95	0	304	35	22	11	30	1.89
3386804--3386846	22	2.0	22	85	0	59	53	2	0	44	1.13
3387401--3387437	15	2.5	15	95	0	65	13	2	0	83	0.74
3399140--3399173	16	2.1	17	94	5	61	35	23	5	35	1.79
3401270--3401302	5	6.6	5	92	0	57	3	36	21	39	1.69
3401620--3401655	2	18.0	2	100	0	72	50	0	0	50	1.00
3401947--3401975	2	14.5	2	100	0	58	51	0	0	48	1.00
3407607--3407641	18	1.9	18	88	0	52	31	11	14	42	1.81
3409741--3409786	2	23.0	2	95	0	83	47	0	2	50	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3410030--3410060	3	10.3	3	100	0	62	67	0	0	32	0.91
3419016--3419071	21	2.6	21	88	2	67	33	23	3	39	1.72
3419027--3419071	21	2.1	21	95	0	81	33	24	4	37	1.76
3419759--3419814	27	2.1	27	89	0	85	30	17	12	39	1.87
3419851--3419884	6	5.7	6	100	0	68	29	0	52	17	1.45
3420571--3420603	2	17.0	2	93	6	59	48	0	0	51	1.00
3422284--3422320	13	3.0	13	92	7	60	51	0	0	48	1.00
3422340--3422372	15	2.1	17	88	11	52	30	0	9	60	1.27
3422616--3422652	18	2.1	18	94	0	65	59	0	29	10	1.31
3423366--3423438	17	4.6	15	78	10	58	35	1	1	61	1.13

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