genome.fa.s8.2.7.7.80.10.50.1000.26.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   

This is table  26  of  33  ( 3942 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)
4499703--4499762	29	2.0	30	90	6	95	0	10	5	85	0.75
4510096--4510126	2	15.5	2	100	0	62	51	48	0	0	1.00
4512089--4512133	19	2.5	18	82	10	56	55	8	0	35	1.31
4514589--4514640	15	3.4	15	77	15	61	46	3	0	50	1.20
4514585--4514649	33	1.9	34	84	9	89	46	4	0	49	1.22
4521220--4521280	29	2.2	29	79	5	72	52	0	0	47	1.00
4532117--4532154	2	19.0	2	100	0	76	50	0	0	50	1.00
4546703--4546746	22	2.0	22	86	8	63	79	11	9	0	0.93
4546717--4546749	13	2.8	12	90	9	50	84	9	6	0	0.76
4553995--4554038	22	2.0	22	86	8	63	40	0	0	59	0.98
4565142--4565173	2	16.0	2	100	0	64	50	0	0	50	1.00
4588627--4588692	33	2.0	33	96	0	123	59	9	19	12	1.59
4594609--4594677	28	2.5	26	82	13	93	57	0	1	40	1.07
4594638--4594684	21	2.2	22	84	3	60	57	0	2	40	1.11
4595324--4595348	2	12.5	2	100	0	50	48	0	0	52	1.00
4608907--4608965	23	2.6	22	82	15	68	67	6	3	22	1.29
4608907--4608965	22	2.7	20	84	12	64	67	6	3	22	1.29
4611100--4611156	30	1.9	29	89	3	87	26	12	22	38	1.89
4623095--4623133	19	2.2	17	90	9	60	61	0	2	35	1.10
4623641--4623681	13	3.2	13	80	16	50	41	4	2	51	1.36
4627413--4627446	6	5.7	6	96	0	59	17	79	0	2	0.86
4634077--4634126	14	3.2	16	72	13	50	44	2	0	54	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4634110--4634165	29	1.9	29	85	7	78	46	1	0	51	1.11
4634985--4635049	31	2.1	30	82	5	76	47	1	0	50	1.10
4635047--4635083	11	3.4	11	84	0	56	32	0	0	67	0.91
4635210--4635234	3	8.3	3	100	0	50	32	32	0	36	1.58
4635872--4635923	16	2.9	18	75	18	56	67	0	0	32	0.91
4636492--4636564	29	2.4	29	84	11	85	39	0	0	60	0.97
4636492--4636564	15	4.8	15	70	23	55	39	0	0	60	0.97
4636509--4636564	29	1.9	29	89	7	87	39	0	0	60	0.97
4636489--4636571	29	3.0	29	73	18	77	42	0	0	57	0.98
4638110--4638163	5	10.4	5	80	7	54	68	0	0	31	0.90
4638110--4638139	11	2.8	11	95	5	53	73	0	0	26	0.84
4638110--4638289	22	8.6	20	68	17	73	60	0	0	38	1.06
4644810--4644883	37	2.0	36	82	10	87	35	20	5	39	1.75
4645371--4645410	2	20.0	2	94	0	71	47	0	0	52	1.00
4651354--4651396	20	2.2	19	83	8	50	44	4	0	51	1.22
4658837--4658868	2	16.5	2	93	6	57	46	0	0	53	1.00
4661452--4661476	2	12.5	2	100	0	50	52	0	0	48	1.00
4661823--4661860	20	2.0	20	89	5	60	68	0	7	23	1.16
4668663--4668698	18	2.1	18	94	5	65	69	0	0	30	0.89
4668669--4668733	22	3.0	21	76	10	60	61	3	0	35	1.12
4668877--4668910	2	17.0	2	100	0	68	50	0	0	50	1.00
4669395--4669432	16	2.4	16	91	4	60	47	2	0	50	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4671748--4671788	18	2.3	18	87	4	57	56	7	2	34	1.40
4672669--4672729	29	2.1	30	84	3	79	45	1	1	50	1.21
4682075--4682122	16	3.2	16	80	14	57	37	0	0	62	0.95
4683577--4683624	21	2.3	20	75	10	51	37	10	8	43	1.69
4688373--4688421	2	25.0	2	95	4	91	0	51	0	48	1.00
4696930--4696963	2	17.0	2	93	0	59	2	47	0	50	1.16
4698024--4698096	37	2.0	37	91	0	119	28	8	6	56	1.55
4701819--4701860	14	3.0	14	85	0	57	54	0	0	45	0.99
4702138--4702187	17	2.8	18	85	8	59	74	10	14	2	1.16
4702138--4702192	18	3.1	17	82	12	58	74	9	14	1	1.14
4702462--4702505	20	2.2	20	84	8	54	4	15	4	75	1.14
4714230--4714259	2	15.0	2	100	0	60	50	0	0	50	1.00
4714416--4714476	21	2.9	21	75	7	52	62	0	0	37	0.96
4714512--4714554	22	2.0	23	90	9	72	60	0	0	39	0.97
4714511--4714562	22	2.3	21	78	12	59	63	0	0	36	0.95
4714885--4714921	3	12.3	3	100	0	74	0	32	0	67	0.91
4715628--4715679	17	3.0	17	94	2	86	84	0	0	15	0.62
4715631--4715682	4	14.5	4	81	18	62	82	0	0	17	0.66
4716403--4716432	9	3.2	9	90	9	51	86	0	0	13	0.57
4717770--4717805	16	2.4	15	86	13	56	80	2	0	16	0.83
4724560--4724687	6	21.5	6	67	17	63	63	0	0	36	0.95
4724566--4724687	39	3.1	37	78	14	104	63	0	0	36	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4724624--4724683	13	4.6	13	70	13	52	68	0	0	31	0.90
4724624--4724694	25	2.8	25	79	12	81	67	1	0	30	0.99
4724625--4724687	11	5.5	11	75	14	56	68	0	0	31	0.90
4725525--4725580	22	2.5	23	80	8	71	39	0	0	60	0.97
4726321--4726553	129	1.8	129	88	1	360	41	20	24	14	1.89
4726747--4726786	21	1.9	21	94	0	71	42	17	30	10	1.82
4727836--4727874	20	2.0	20	85	10	53	48	0	2	48	1.15
4729215--4729242	12	2.3	12	100	0	56	50	7	0	42	1.30
4731493--4731545	18	3.1	18	82	12	58	49	0	0	50	1.00
4731728--4731784	21	2.7	21	76	18	64	52	1	3	42	1.28
4732604--4732648	20	2.2	20	84	7	56	48	0	0	51	1.00
4732620--4732708	35	2.5	35	75	10	101	51	0	1	47	1.08
4732712--4732750	12	3.0	12	88	11	51	35	0	0	64	0.94
4740602--4740626	10	2.5	10	100	0	50	28	8	32	32	1.86
4742549--4742599	26	2.0	26	100	0	102	25	11	19	43	1.85
4746043--4746072	2	15.0	2	100	0	60	50	0	0	50	1.00
4748605--4748638	11	2.9	12	82	8	52	64	0	2	32	1.08
4750211--4750235	5	5.0	5	100	0	50	60	0	0	40	0.97
4752250--4752296	20	2.2	22	85	14	64	65	10	10	12	1.46
4754990--4755023	6	5.7	6	92	0	59	17	17	11	52	1.73
4756140--4756190	16	3.2	16	72	5	50	1	29	1	66	1.13
4757394--4757422	3	9.7	3	100	0	58	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4757825--4757879	25	2.1	27	83	6	69	54	0	3	41	1.18
4769918--4769950	2	16.5	2	100	0	66	51	0	48	0	1.00
4771357--4771393	3	12.3	3	94	0	65	64	0	0	35	0.94
4775559--4775593	2	17.5	2	93	0	61	48	2	0	48	1.16
4781716--4781761	24	1.9	24	86	0	65	50	6	28	15	1.69
4782111--4782149	20	2.0	20	85	10	53	64	0	0	35	0.94
4783696--4783722	5	5.4	5	100	0	54	81	0	18	0	0.69
4785275--4785299	1	25.0	1	100	0	50	0	0	0	100	0.00
4787276--4787300	2	12.5	2	100	0	50	48	0	0	52	1.00
4789051--4789088	2	19.0	2	94	0	67	47	2	0	50	1.15
4793513--4793564	2	26.0	2	100	0	104	50	0	0	50	1.00
4797689--4797718	2	15.0	2	100	0	60	50	0	0	50	1.00
4797960--4798030	11	6.3	11	74	16	56	57	0	0	42	0.98
4798452--4798487	2	18.0	2	100	0	72	50	0	0	50	1.00
4800131--4800168	12	3.2	12	92	0	58	28	2	36	31	1.71
4802324--4802372	23	2.1	23	88	0	71	42	0	4	53	1.20
4802469--4802512	18	2.2	21	88	11	67	36	0	0	63	0.95
4803018--4803075	28	2.0	29	83	6	73	53	0	1	44	1.10
4803053--4803086	16	2.1	16	88	0	50	55	0	0	44	0.99
4803029--4803082	28	1.9	28	85	7	74	53	0	0	46	1.00
4805472--4805661	105	1.8	105	85	8	271	28	25	15	30	1.96
4813861--4814114	132	1.9	133	93	1	438	18	12	16	51	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4817798--4817824	13	2.1	13	100	0	54	22	7	33	37	1.82
4825137--4825166	2	15.0	2	92	0	51	50	46	3	0	1.18
4825503--4825546	17	2.7	17	80	19	58	81	6	6	4	0.97
4826717--4826768	22	2.3	23	86	3	70	42	0	0	57	0.98
4826711--4826866	13	12.3	12	69	20	88	37	0	1	60	1.05
4826789--4826865	5	15.4	5	72	20	63	36	0	0	63	0.95
4826789--4826865	27	2.7	30	82	17	110	36	0	0	63	0.95
4836588--4836632	18	2.5	18	81	0	54	46	20	2	31	1.62
4837095--4837518	167	2.6	163	89	5	606	38	13	17	31	1.88
4838357--4838385	2	14.5	2	100	0	58	51	0	48	0	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   32   
          33