genome.fa.s7.2.7.7.80.10.50.1000.24.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: Scaffold7
Parameters: 2 7 7 80 10 50 1000
Length:  6555642

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   

This is table  24  of  37  ( 4421 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)
4165358--4165425	33	2.1	33	86	5	93	42	16	11	29	1.83
4167462--4167542	42	1.9	43	97	2	155	50	13	6	29	1.66
4167828--4167954	49	2.7	46	78	7	139	30	19	25	23	1.98
4168017--4168630	58	10.6	58	87	4	674	21	18	30	29	1.97
4168012--4168623	265	2.3	257	87	4	870	22	17	30	29	1.97
4168012--4168630	28	21.4	28	81	7	630	22	17	30	29	1.97
4169380--4169405	13	2.0	13	100	0	52	30	15	15	38	1.88
4169444--4169519	21	3.7	21	80	3	100	28	17	11	42	1.84
4169465--4169537	20	3.6	20	81	3	101	31	19	13	35	1.91
4169444--4169537	41	2.3	41	98	0	179	29	18	12	39	1.88
4171989--4172027	13	3.0	13	96	0	69	35	15	17	30	1.91
4172013--4172091	20	3.7	20	75	18	70	45	15	13	25	1.83
4174099--4174136	15	2.5	15	91	0	58	13	21	15	50	1.78
4178199--4178224	13	2.0	13	100	0	52	30	15	15	38	1.88
4178263--4178338	21	3.7	21	80	3	100	28	17	11	42	1.84
4178284--4178356	20	3.6	20	81	3	101	31	19	13	35	1.91
4178263--4178356	41	2.3	41	98	0	179	29	18	12	39	1.88
4178657--4178852	30	6.6	29	77	12	200	22	18	30	28	1.98
4178649--4178852	60	3.4	59	88	1	309	22	19	29	28	1.98
4180066--4180120	10	5.8	9	81	10	56	1	3	14	80	0.94
4180053--4180122	10	7.2	9	75	16	52	2	2	15	78	0.99
4183340--4183366	13	2.1	13	100	0	54	29	14	14	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4183352--4183407	19	2.8	21	86	8	80	33	14	17	33	1.90
4183323--4183385	32	1.9	33	87	3	92	28	17	15	38	1.91
4198508--4198633	20	5.8	20	74	18	117	42	12	15	29	1.84
4201584--4201623	21	1.9	21	89	0	62	15	2	27	55	1.53
4203122--4203198	21	3.7	21	89	3	111	35	12	16	35	1.88
4203234--4203301	19	3.9	19	76	21	76	35	11	16	36	1.85
4203255--4203279	13	1.9	13	100	0	50	36	16	16	32	1.90
4203236--4203298	32	2.0	32	93	0	108	34	12	17	34	1.88
4203341--4203366	13	2.0	13	100	0	52	30	15	15	38	1.88
4218338--4218379	11	3.6	11	90	9	66	88	9	2	0	0.61
4218338--4218379	12	3.6	12	87	3	59	88	9	2	0	0.61
4219526--4219615	26	3.3	26	65	14	65	28	31	17	22	1.97
4219694--4219779	27	3.1	27	62	15	68	27	30	18	23	1.98
4219389--4219917	55	9.6	55	92	2	859	28	29	19	22	1.98
4220705--4220759	19	2.9	19	91	0	92	36	9	14	40	1.78
4220799--4220824	13	2.0	13	100	0	52	30	15	15	38	1.88
4223239--4223290	27	2.0	25	85	10	70	30	32	15	21	1.94
4223249--4223313	28	2.4	27	84	7	78	26	38	15	20	1.92
4227039--4227106	35	2.0	35	97	2	129	33	11	25	29	1.91
4231700--4231736	19	1.9	19	94	0	65	48	13	10	27	1.75
4231867--4231912	16	2.8	17	74	9	51	41	23	17	17	1.90
4233271--4233732	28	16.1	28	79	9	450	30	30	16	22	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4233838--4233969	48	2.8	48	89	0	192	20	25	17	37	1.94
4234775--4234850	20	3.8	20	73	3	82	32	11	11	43	1.78
4234724--4234890	90	1.9	90	88	0	253	29	13	10	46	1.76
4248095--4248125	13	2.4	13	94	0	53	35	16	12	35	1.87
4248079--4248145	33	2.0	33	85	5	91	34	11	17	35	1.87
4254311--4254335	13	1.9	13	100	0	50	32	20	16	32	1.94
4256844--4256894	20	2.6	20	87	3	68	35	13	15	35	1.87
4256924--4256976	20	2.7	20	100	0	106	33	15	18	32	1.92
4256959--4256989	13	2.4	13	94	0	53	35	16	12	35	1.87
4256939--4257009	33	2.2	33	84	5	90	35	15	16	32	1.91
4259965--4260017	9	5.6	10	72	20	51	54	0	0	45	0.99
4259965--4260024	19	3.4	18	72	17	54	56	0	0	43	0.99
4260001--4260043	16	2.8	16	92	3	70	74	0	0	25	0.82
4260001--4260039	8	4.8	9	79	20	50	71	0	0	28	0.86
4260022--4260050	13	2.3	13	94	5	51	75	0	0	24	0.80
4260069--4260106	15	2.6	14	87	4	58	0	10	5	84	0.77
4260361--4260391	8	4.0	8	91	8	55	0	9	0	90	0.46
4264280--4264326	21	2.2	22	84	3	60	59	2	8	29	1.39
4264639--4264679	15	2.6	16	82	14	50	53	0	0	46	1.00
4265406--4265439	4	8.2	4	87	6	50	23	5	0	70	1.09
4266140--4266185	22	2.0	22	83	4	56	60	0	0	39	0.97
4266146--4266193	22	2.1	23	85	11	64	56	0	0	43	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4266400--4266441	3	14.0	3	100	0	84	66	0	0	33	0.92
4266442--4266467	3	8.7	3	100	0	52	34	0	0	65	0.93
4266645--4266718	38	1.9	38	81	5	87	44	1	0	54	1.08
4269819--4269897	31	2.4	34	75	20	85	41	1	0	56	1.07
4270007--4270063	27	2.1	27	93	0	96	52	3	10	33	1.53
4270369--4270396	2	14.0	2	100	0	56	50	0	0	50	1.00
4273306--4273360	15	3.6	16	70	7	51	47	0	0	52	1.00
4273318--4273375	30	1.9	30	86	6	82	41	0	0	58	0.98
4273327--4273398	30	2.3	31	78	7	74	50	1	0	48	1.09
4276885--4276971	18	4.6	18	68	18	68	52	11	11	24	1.70
4276895--4276970	20	3.8	20	68	14	68	56	10	11	21	1.64
4276883--4277027	40	3.7	40	74	7	100	55	8	11	24	1.64
4277102--4277153	19	2.7	19	85	5	70	40	15	11	32	1.83
4278679--4278723	23	2.0	23	86	0	63	37	0	17	44	1.49
4280170--4280220	13	3.9	13	84	0	66	37	17	11	33	1.86
4282918--4282956	13	2.9	13	88	3	60	38	12	12	35	1.82
4287056--4287096	21	1.9	22	85	5	57	24	17	2	56	1.53
4287923--4287973	20	2.5	20	87	6	68	33	15	11	39	1.84
4288800--4288972	76	2.3	77	93	3	296	28	22	6	41	1.80
4291679--4291705	13	2.1	13	100	0	54	29	14	14	40	1.86
4291690--4291745	19	2.9	19	89	2	85	30	17	14	37	1.90
4293410--4293444	12	2.9	12	95	0	61	45	0	25	28	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4296604--4296656	20	2.7	20	85	5	63	33	20	13	32	1.91
4296687--4296730	20	2.2	20	88	4	63	36	11	18	34	1.86
4296766--4296792	13	2.1	13	100	0	54	40	14	14	29	1.86
4306660--4306907	73	3.5	72	79	7	263	41	14	16	26	1.88
4306801--4306950	72	2.1	73	83	8	191	40	14	19	26	1.89
4307000--4307082	42	2.0	42	95	0	148	39	14	7	38	1.74
4307901--4307960	27	2.2	27	85	5	77	70	3	16	10	1.29
4308110--4308165	26	2.2	26	80	6	60	12	5	8	73	1.24
4316039--4316090	19	2.6	19	90	6	77	75	1	19	3	1.06
4316040--4316088	20	2.5	20	83	16	66	73	2	20	4	1.10
4316331--4316377	10	4.7	10	78	0	58	82	0	12	4	0.80
4320176--4320460	155	1.8	155	81	4	360	28	14	15	42	1.85
4322472--4322503	16	2.0	16	93	0	55	15	12	6	65	1.44
4328136--4328814	60	11.4	60	75	6	438	19	16	17	47	1.83
4328144--4328804	119	5.6	118	78	4	573	19	16	17	47	1.83
4328611--4328843	60	3.9	59	75	8	186	20	13	17	49	1.79
4329099--4329193	47	2.0	47	84	8	122	29	24	6	40	1.80
4329796--4329894	41	2.4	40	73	6	90	22	20	13	44	1.85
4330066--4330099	16	2.2	16	89	5	52	17	29	8	44	1.79
4334854--4334887	11	2.9	12	82	8	52	23	0	5	70	1.09
4335856--4335916	30	2.0	30	83	0	77	32	8	6	52	1.57
4336101--4336147	2	23.5	2	100	0	94	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)
4337659--4337793	68	2.0	69	84	7	177	43	4	4	47	1.43
4338256--4338280	7	3.6	7	100	0	50	56	0	0	44	0.99
4338339--4338383	23	1.9	24	81	4	56	64	0	2	33	1.06
4338391--4338439	15	3.3	15	77	11	55	42	0	0	57	0.99
4338391--4338439	8	6.5	8	75	11	50	42	0	0	57	0.99
4338391--4338450	13	4.8	13	72	27	51	41	0	1	56	1.09
4338547--4338573	14	1.9	14	100	0	54	74	3	0	22	0.98
4338903--4338930	4	7.0	4	100	0	56	25	0	0	75	0.81
4338932--4338984	22	2.3	23	78	21	58	45	3	3	47	1.39
4339039--4339553	221	2.3	223	82	7	571	46	6	5	41	1.52

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