genome.fa.s2.2.7.7.80.10.50.1000.21.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  21  of  38  ( 4457 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)
3223463--3223527	25	2.6	25	90	0	94	40	0	21	38	1.54
3227267--3227395	52	2.5	52	92	0	222	27	19	17	35	1.94
3228195--3228250	20	2.8	20	88	0	76	39	10	10	39	1.75
3231667--3231708	21	2.0	20	86	4	57	78	2	11	7	1.04
3231731--3231776	7	6.4	7	84	2	56	76	0	19	4	0.96
3231731--3231776	21	2.1	22	92	4	76	76	0	19	4	0.96
3232026--3232068	10	4.3	10	78	0	50	79	2	16	2	0.95
3233405--3233448	22	2.1	22	87	8	65	40	11	4	43	1.61
3234104--3234131	14	2.0	14	100	0	56	21	28	14	35	1.92
3234222--3234347	56	2.2	56	94	0	216	34	20	8	36	1.84
3238241--3238309	36	1.9	36	85	2	95	24	24	13	37	1.91
3238853--3238877	13	1.9	13	100	0	50	36	16	16	32	1.90
3238835--3238898	33	2.0	32	87	9	94	39	15	15	29	1.89
3239665--3239694	13	2.3	13	94	0	51	36	10	16	36	1.82
3249207--3249277	20	3.3	20	70	14	61	16	21	15	46	1.84
3249225--3249297	24	3.2	24	69	15	82	16	20	15	47	1.82
3249207--3249310	44	2.4	44	95	0	190	18	21	14	46	1.84
3249381--3249451	20	3.4	20	74	11	61	26	14	15	43	1.85
3249951--3250232	89	3.2	88	82	7	353	30	29	10	28	1.91
3249951--3250266	89	3.6	88	78	9	342	31	29	10	28	1.91
3250123--3250292	89	1.9	89	79	4	191	32	27	12	27	1.93
3250494--3250572	35	2.3	35	90	0	122	25	29	8	36	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3250592--3250735	46	3.1	46	79	10	157	21	20	18	39	1.92
3250586--3250708	48	2.6	47	81	8	144	20	21	16	41	1.90
3250793--3250954	44	3.7	44	72	9	141	19	19	16	43	1.88
3250786--3250999	88	2.4	88	85	1	286	18	22	16	42	1.89
3250795--3250999	44	4.7	44	70	7	130	19	22	16	41	1.89
3251159--3251392	42	5.6	42	79	0	189	15	26	19	38	1.91
3251148--3251424	84	3.3	84	78	0	221	17	27	19	36	1.94
3251248--3251424	42	4.2	42	76	4	142	19	27	18	35	1.95
3251617--3251701	39	2.1	41	91	4	138	22	31	8	37	1.84
3252689--3252995	167	1.8	166	83	0	407	28	9	8	53	1.63
3252744--3253239	167	3.0	164	81	6	497	29	10	10	50	1.70
3252948--3253306	164	2.2	166	86	5	487	29	11	10	47	1.74
3253773--3253817	24	1.9	23	86	4	63	71	2	24	2	1.09
3253800--3253835	9	3.9	9	85	7	54	75	2	13	8	1.15
3254802--3255229	168	2.6	164	82	5	508	34	11	11	41	1.78
3255343--3255880	156	3.5	153	79	4	558	23	17	20	39	1.93
3262321--3262359	13	3.0	13	88	0	60	35	12	17	33	1.88
3262346--3262398	20	2.7	20	91	5	81	47	15	15	22	1.82
3265567--3265639	20	3.6	20	81	3	101	36	13	17	31	1.89
3265584--3265660	21	3.7	21	79	6	95	44	11	15	28	1.82
3265567--3265660	41	2.3	41	96	3	172	40	12	17	29	1.86
3265699--3265724	13	2.0	13	100	0	52	38	15	15	30	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3269785--3269815	15	2.1	15	93	0	53	48	16	22	12	1.80
3271894--3271931	13	2.9	13	96	0	67	34	18	15	31	1.92
3272052--3272098	21	2.3	21	79	20	55	34	23	4	38	1.74
3272054--3272096	20	2.2	19	84	16	52	32	23	4	39	1.75
3274373--3274445	20	3.6	20	81	3	101	36	13	17	31	1.89
3274390--3274466	21	3.7	21	79	6	95	44	11	15	28	1.82
3274373--3274466	41	2.3	41	96	3	172	40	12	17	29	1.86
3274505--3274530	13	2.0	13	100	0	52	38	15	15	30	1.88
3276647--3276708	31	2.0	31	100	0	124	19	19	9	51	1.74
3281966--3282073	50	2.2	50	85	5	139	28	18	12	39	1.88
3284420--3284859	79	5.6	79	83	1	506	27	25	13	33	1.93
3284429--3284858	237	1.8	237	84	4	598	27	25	13	33	1.93
3286261--3286363	52	2.0	52	86	0	143	33	13	25	27	1.93
3286271--3286456	96	1.9	96	81	2	221	32	16	23	26	1.96
3286862--3286994	34	4.0	33	78	9	128	27	16	28	27	1.97
3286642--3286994	33	10.6	33	74	10	197	25	16	29	28	1.96
3294167--3294430	32	8.2	31	77	8	219	29	28	18	23	1.98
3294153--3294430	64	4.3	64	77	7	267	30	28	18	22	1.98
3294202--3294422	97	2.3	96	82	5	259	31	28	17	23	1.96
3294589--3294696	52	2.1	52	82	0	126	25	24	13	36	1.93
3294677--3294815	61	2.3	61	83	5	174	23	23	15	37	1.93
3296960--3297034	20	3.8	20	92	3	98	30	14	13	41	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3299090--3300272	593	2.0	591	92	0	1979	28	22	12	36	1.90
3308454--3308530	20	3.7	20	80	10	82	41	11	19	27	1.86
3310124--3310229	47	2.2	48	81	1	124	33	13	15	38	1.86
3310567--3310634	3	24.0	3	73	11	63	67	1	1	29	1.08
3310564--3310648	14	6.4	14	67	25	51	68	1	1	29	1.05
3310561--3310650	39	2.2	42	82	7	114	68	1	1	28	1.03
3310746--3310778	17	1.9	17	100	0	66	18	21	12	48	1.80
3310952--3311005	23	2.3	23	80	0	72	42	22	16	18	1.89
3311135--3311195	28	2.1	28	85	8	79	73	9	13	3	1.20
3311201--3311301	30	3.5	29	72	18	77	72	9	12	4	1.26
3311257--3311305	24	2.0	25	84	4	64	77	8	10	4	1.10
3314892--3315095	42	4.8	42	75	7	137	19	20	13	46	1.83
3315018--3315118	43	2.4	43	81	1	114	21	22	10	44	1.83
3315143--3316027	42	21.4	41	71	10	306	16	24	18	40	1.90
3315143--3316046	84	10.9	83	70	11	418	16	24	18	40	1.90
3315143--3315734	204	2.9	203	76	8	497	16	24	19	40	1.91
3315143--3316004	126	7.0	126	71	12	473	16	24	18	40	1.90
3319766--3320093	52	6.4	51	80	5	322	23	25	17	33	1.96
3319766--3320044	101	2.8	101	88	0	405	23	24	18	33	1.97
3319766--3320043	49	5.4	52	82	5	325	23	24	18	33	1.96
3319993--3320140	52	2.8	53	74	7	129	25	26	14	34	1.94
3320797--3320844	13	3.4	13	74	20	51	35	10	16	37	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3320784--3320846	30	2.0	31	93	6	110	34	9	17	38	1.82
3320780--3320838	17	3.6	17	73	21	63	35	11	15	37	1.84
3320863--3320903	21	2.0	21	95	0	73	41	9	21	26	1.84
3323245--3323381	52	2.6	52	88	2	204	32	24	10	32	1.90
3323361--3323435	27	2.7	27	89	6	107	24	33	20	22	1.97
3323392--3323749	79	4.5	79	86	4	472	27	25	14	32	1.95
3323388--3323749	157	2.3	158	87	1	530	27	25	14	32	1.95
3324910--3324934	13	1.9	13	100	0	50	36	16	16	32	1.90
3340190--3340266	28	2.8	28	91	0	118	23	31	22	23	1.99
3342317--3342343	4	6.8	4	100	0	54	22	0	0	77	0.76
3351215--3351292	32	2.4	32	86	0	102	32	16	15	35	1.90
3351247--3351271	13	1.9	13	100	0	50	32	16	16	36	1.90
3352163--3352725	52	11.7	49	75	12	443	31	17	25	25	1.97
3352111--3352765	101	6.7	100	76	11	404	31	17	25	25	1.97
3352157--3352451	150	2.0	150	88	0	446	32	16	24	26	1.96
3352415--3352573	39	3.8	39	76	13	156	27	20	26	25	1.99
3352452--3352730	48	5.9	48	73	13	211	31	17	26	24	1.97
3352362--3352626	87	3.0	87	89	3	379	28	20	26	24	1.99
3352539--3352765	52	4.4	52	76	6	198	33	16	25	24	1.96
3352948--3352986	21	1.9	20	94	5	69	35	20	12	30	1.90
3353042--3353162	13	7.9	13	69	28	62	35	12	17	34	1.87
3353023--3353189	32	5.2	32	96	0	307	34	11	17	35	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3353023--3353225	96	2.1	96	86	5	279	34	13	18	33	1.89
3356396--3356513	49	2.4	49	78	2	132	35	16	25	22	1.94
3356509--3356617	30	3.7	30	83	12	127	18	19	28	33	1.95
3356591--3356840	34	8.0	34	78	14	229	33	12	34	20	1.90
3356632--3356712	27	3.0	27	87	3	110	29	13	33	23	1.93
3356591--3356867	61	4.5	61	79	13	336	32	12	34	20	1.90
3356747--3356870	27	4.3	27	79	13	140	30	12	36	20	1.89
3358328--3358357	12	2.6	12	94	5	53	0	0	13	86	0.57
3369550--3369604	27	2.0	27	100	0	110	23	14	36	25	1.93
3371853--3371915	19	3.7	18	74	24	64	34	15	14	34	1.88

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