genome.fa.s64.2.7.7.80.10.50.1000.17.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   

This is table  17  of  45  ( 5312 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)
3165089--3165144	29	1.9	29	82	7	69	39	0	0	60	0.97
3169002--3169036	17	2.1	18	89	10	56	34	0	0	65	0.93
3170970--3171000	4	7.8	4	100	0	62	74	0	0	25	0.82
3171372--3171438	18	3.7	20	79	15	65	44	0	0	55	0.99
3171372--3171445	33	2.1	34	85	9	96	47	0	0	52	1.00
3171389--3171465	33	2.3	33	82	10	86	48	0	0	51	1.00
3171417--3171479	19	2.8	22	72	22	60	50	0	0	49	1.00
3171471--3171514	11	3.9	11	85	11	54	34	0	0	65	0.93
3171780--3171833	5	10.4	5	84	7	72	75	1	0	22	0.89
3171780--3171834	11	5.2	11	88	2	69	76	1	0	21	0.88
3172276--3172340	28	2.4	30	75	19	70	36	3	3	56	1.30
3172490--3172533	19	2.3	19	81	14	54	38	0	0	61	0.96
3172564--3172609	13	3.6	13	77	11	51	32	0	0	67	0.91
3172557--3172589	17	2.0	16	94	5	57	36	0	0	63	0.95
3175006--3175087	41	2.0	41	92	0	137	29	9	17	43	1.80
3177774--3177806	2	16.5	2	100	0	66	48	0	0	51	1.00
3178614--3178690	17	4.8	17	76	12	58	53	0	0	46	1.00
3180059--3180110	3	17.0	3	88	4	77	67	0	1	30	1.02
3180302--3180368	27	2.6	27	79	11	68	49	0	1	49	1.10
3180298--3180368	25	2.7	26	78	10	65	47	0	1	50	1.09
3181317--3181373	10	5.9	10	74	15	57	59	0	1	38	1.08
3181317--3181375	19	3.1	19	83	9	75	61	0	1	37	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3181329--3181444	43	2.7	43	76	15	121	53	0	2	43	1.20
3181367--3181475	7	16.0	7	66	25	56	51	0	2	44	1.22
3181382--3181444	15	4.4	14	76	11	56	50	1	1	46	1.20
3181428--3181470	20	2.1	21	83	12	54	53	0	2	44	1.13
3182134--3182216	29	2.7	31	76	12	84	39	1	3	55	1.25
3182213--3182266	23	2.3	23	90	0	81	57	3	0	38	1.17
3182204--3182266	23	2.8	22	83	7	72	53	3	0	42	1.16
3185767--3185856	30	3.0	28	76	12	83	38	2	1	57	1.18
3186701--3186737	18	2.1	18	89	0	56	37	2	0	59	1.12
3187049--3187081	17	1.9	17	88	11	50	48	6	0	45	1.27
3187000--3187074	40	1.9	40	81	10	93	54	1	0	44	1.08
3188795--3188891	22	4.4	21	70	20	72	59	1	0	39	1.04
3188788--3188880	47	2.0	48	82	6	118	59	2	0	38	1.10
3193555--3193586	2	16.0	2	93	0	55	53	0	0	46	1.00
3194722--3194894	90	1.9	90	89	4	271	42	5	6	45	1.52
3198027--3198086	29	2.1	29	96	0	111	31	10	18	40	1.84
3198093--3198138	19	2.4	19	85	10	58	47	0	0	52	1.00
3198100--3198144	13	3.7	13	80	11	51	44	0	0	55	0.99
3200446--3200479	16	2.1	16	88	0	50	58	2	0	38	1.13
3203358--3203396	11	3.7	11	80	13	55	51	0	0	48	1.00
3203361--3203398	20	1.9	20	100	0	76	50	0	0	50	1.00
3204761--3204798	20	1.9	20	84	10	51	36	10	5	47	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3209107--3209152	24	1.9	24	81	0	56	32	2	2	63	1.19
3210072--3210099	2	14.0	2	100	0	56	50	0	50	0	1.00
3216909--3216996	17	5.1	17	75	14	83	59	0	1	39	1.05
3216911--3216994	32	2.6	33	85	10	104	59	0	1	39	1.05
3218069--3218110	22	1.9	22	90	9	68	61	0	0	38	0.96
3218069--3218123	22	2.6	22	80	11	62	58	0	0	41	0.98
3218118--3218160	21	2.0	20	83	16	52	48	0	0	51	1.00
3221613--3221666	19	2.8	19	72	10	65	20	12	25	40	1.88
3222048--3222106	26	2.2	27	82	8	68	44	0	1	54	1.10
3222955--3223033	29	2.7	30	79	16	103	55	0	0	44	0.99
3226457--3226515	23	2.7	23	75	15	61	40	0	0	59	0.97
3226476--3226539	30	2.1	30	83	11	78	46	1	0	51	1.10
3226476--3226559	30	2.8	30	77	16	77	47	2	0	50	1.14
3231299--3231418	5	22.8	5	67	14	55	60	0	0	38	1.09
3233854--3233886	13	2.4	14	90	10	50	57	0	0	42	0.98
3236044--3236097	28	2.0	27	86	13	76	50	0	0	50	1.00
3236052--3236109	29	2.0	28	86	3	80	58	0	0	41	0.98
3237845--3237878	11	2.9	12	86	8	52	73	5	20	0	1.04
3238064--3238097	3	11.3	3	100	0	68	67	0	0	32	0.91
3240204--3240264	29	2.1	30	87	3	88	42	0	3	54	1.17
3240288--3240344	12	5.0	12	70	12	57	56	0	1	42	1.10
3240286--3240381	22	4.5	20	73	22	70	55	1	2	41	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3240288--3240363	22	3.4	23	83	10	95	57	0	2	39	1.12
3240337--3240435	37	2.7	38	71	17	93	58	2	1	38	1.16
3240460--3240498	10	3.6	10	81	18	51	48	0	0	51	1.00
3240465--3240501	12	3.2	12	84	7	58	48	0	0	51	1.00
3240461--3240495	11	3.1	11	84	8	52	54	0	0	45	0.99
3240472--3240533	30	2.1	30	88	11	92	43	0	0	56	0.99
3240815--3240881	6	11.2	6	72	15	50	38	0	0	61	0.96
3240815--3240884	24	2.9	25	81	12	76	38	0	0	61	0.96
3240812--3240914	10	10.9	10	73	18	62	35	0	0	63	1.01
3240811--3240891	30	2.5	32	82	7	94	39	0	0	60	0.97
3240879--3240933	21	2.5	22	76	2	58	36	1	0	61	1.06
3240894--3240959	27	2.5	26	78	4	80	39	0	0	60	0.97
3240907--3240970	30	2.3	27	84	13	76	40	0	0	59	0.97
3247377--3247427	21	2.5	21	90	6	79	35	0	0	64	0.94
3247806--3247843	2	19.0	2	100	0	76	50	0	0	50	1.00
3248468--3248515	22	2.2	23	85	7	64	41	10	2	45	1.50
3250178--3250238	24	2.5	24	83	0	77	19	22	24	32	1.97
3253197--3253234	2	19.0	2	100	0	76	50	0	50	0	1.00
3259830--3259904	32	2.3	31	82	8	87	44	1	1	53	1.17
3269968--3269998	2	15.5	2	100	0	62	48	0	0	51	1.00
3270958--3271004	9	4.8	9	82	17	58	53	0	0	46	1.00
3270947--3271004	19	2.9	19	85	10	55	53	1	0	44	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3270958--3271040	30	2.7	30	82	10	98	49	3	1	45	1.27
3270958--3271009	21	2.5	20	87	9	70	50	1	0	48	1.12
3271931--3272013	24	3.6	23	71	18	64	48	0	0	51	1.00
3271936--3271984	24	2.0	25	88	8	73	53	0	0	46	1.00
3271941--3272009	22	2.9	25	77	16	74	47	0	0	52	1.00
3272217--3272267	23	2.3	22	80	6	59	58	0	3	37	1.16
3272252--3272294	21	2.0	22	82	13	54	60	0	0	39	0.97
3272315--3272352	15	2.4	16	82	8	51	63	2	0	34	1.09
3273400--3273471	36	2.0	36	86	2	101	36	9	26	27	1.88
3273400--3273485	35	2.5	34	82	10	104	32	11	24	31	1.91
3279297--3279324	2	14.0	2	100	0	56	50	0	0	50	1.00
3282067--3282107	2	20.5	2	100	0	82	51	48	0	0	1.00
3283601--3283673	31	2.4	31	84	6	87	43	6	4	45	1.49
3284817--3284843	6	4.5	6	100	0	54	85	0	0	14	0.61
3286118--3286149	16	1.9	16	93	6	55	62	3	0	34	1.11
3286273--3286315	21	2.0	21	86	8	61	58	6	2	32	1.38
3298994--3299022	15	1.9	15	100	0	58	31	6	0	62	1.22
3306522--3306590	21	3.3	21	87	2	95	11	24	8	55	1.64
3306905--3306957	27	2.0	27	100	0	106	49	11	7	32	1.67
3306901--3306951	6	9.2	6	77	16	56	49	13	3	33	1.61
3306948--3306975	14	2.0	14	100	0	56	71	0	14	14	1.15
3308804--3308856	25	2.1	26	86	10	74	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)
3309620--3309671	26	2.0	27	82	17	65	23	15	5	55	1.61
3310544--3310610	30	2.2	29	84	5	80	41	5	4	47	1.48
3313733--3313778	24	1.9	24	86	0	65	41	28	6	23	1.79
3313773--3313836	28	2.3	28	89	5	94	53	18	7	20	1.69
3313783--3313837	28	2.0	28	96	0	101	49	20	10	20	1.78
3315733--3315778	21	2.1	22	84	4	58	19	30	19	30	1.97
3321363--3321394	6	5.3	6	100	0	64	50	34	15	0	1.45
3321971--3322011	14	2.8	15	85	3	57	19	4	0	75	0.98
3322921--3322982	19	3.4	19	84	8	76	41	1	0	56	1.09
3322920--3322981	9	6.5	10	73	19	53	41	1	0	56	1.09

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