genome.fa.s1.2.7.7.80.10.50.1000.40.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   46   47   48   
          49   50   51   52   

This is table  40  of  52  ( 6211 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)
6594963--6595091	20	6.9	18	67	21	63	45	1	0	52	1.10
6595015--6595094	29	2.6	29	84	9	88	47	1	0	51	1.08
6595016--6595122	15	7.0	15	71	15	69	43	1	0	54	1.11
6596232--6596265	18	1.9	17	88	5	50	44	0	0	55	0.99
6600624--6600716	34	2.8	34	74	11	93	47	0	0	52	1.00
6602757--6602794	11	3.5	11	86	13	53	63	0	2	34	1.09
6602808--6602868	17	3.5	17	72	16	54	67	1	3	27	1.16
6602812--6602873	11	5.4	12	76	16	51	66	1	3	29	1.17
6604502--6604545	20	2.1	22	91	8	74	70	0	0	29	0.88
6605715--6605754	2	20.0	2	100	0	80	50	0	0	50	1.00
6606152--6606194	10	4.2	10	88	5	59	69	2	0	27	1.00
6611478--6611524	16	3.0	15	87	6	58	44	8	12	34	1.73
6611484--6611529	16	2.9	16	83	0	56	45	10	13	30	1.77
6615136--6615219	23	3.6	22	74	16	64	50	1	2	46	1.22
6615183--6615243	24	2.4	25	78	13	72	50	1	1	45	1.21
6615817--6615857	16	2.6	16	96	0	73	46	26	9	17	1.79
6616357--6616386	16	1.9	15	93	6	51	53	0	16	30	1.44
6618634--6618696	18	3.5	18	82	18	78	52	0	1	46	1.10
6618879--6618931	15	3.3	16	77	15	56	67	11	1	18	1.30
6618873--6618947	32	2.4	32	86	2	98	62	13	1	22	1.38
6618873--6618931	16	3.8	16	78	13	68	66	11	1	20	1.33
6618955--6619015	16	3.8	16	79	12	63	54	22	0	22	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6619723--6619748	2	13.0	2	100	0	52	0	50	0	50	1.00
6624811--6624916	30	3.5	30	69	19	78	39	15	0	44	1.52
6627461--6627643	34	5.4	34	88	0	260	25	7	26	40	1.81
6627461--6627643	102	1.8	101	92	1	312	25	7	26	40	1.81
6627948--6628010	19	3.3	19	90	0	90	28	17	19	34	1.94
6632076--6632260	34	5.5	34	89	0	273	25	7	26	40	1.82
6632076--6632260	102	1.8	101	94	1	325	25	7	26	40	1.82
6640173--6640407	78	3.0	77	78	6	256	26	23	14	35	1.93
6640365--6640435	28	2.5	28	88	0	106	25	29	16	28	1.97
6640285--6640510	107	2.1	106	85	4	296	26	23	16	34	1.95
6640393--6640589	78	2.5	76	85	9	254	26	25	14	33	1.94
6640208--6640691	185	2.6	185	87	4	672	26	23	15	35	1.94
6640551--6640620	28	2.5	28	92	0	113	24	24	18	32	1.97
6640472--6640694	107	2.1	106	87	4	315	25	22	17	34	1.95
6640578--6640747	79	2.2	78	81	8	193	27	22	15	35	1.94
6642921--6642958	16	2.5	15	87	12	51	23	2	2	71	1.12
6644162--6644347	5	36.6	5	70	13	112	58	1	1	39	1.12
6644174--6644228	23	2.5	21	86	13	76	67	1	0	30	1.01
6644189--6644347	13	12.0	13	67	19	55	57	1	1	39	1.14
6644162--6644347	16	12.2	15	69	12	112	58	1	1	39	1.12
6648226--6648269	23	2.0	21	82	8	52	47	0	2	50	1.13
6648226--6648265	21	2.0	20	85	9	55	45	0	2	52	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6648675--6648718	2	23.0	2	81	9	56	50	0	2	47	1.13
6648675--6648732	28	2.1	28	83	6	73	53	1	5	39	1.33
6649413--6649450	20	2.0	20	89	5	60	50	0	0	50	1.00
6650753--6650782	13	2.2	14	94	5	53	73	0	3	23	0.98
6650980--6651128	5	30.8	5	65	21	52	39	0	0	59	1.02
6650979--6651123	17	8.9	17	70	22	91	39	0	0	60	1.02
6651010--6651075	18	4.5	15	70	22	50	40	0	0	59	0.98
6651022--6651086	18	3.7	18	76	21	75	40	0	0	60	0.97
6651005--6651121	52	2.2	52	82	11	141	40	0	0	59	0.97
6651082--6651142	22	2.8	21	81	16	63	37	0	1	60	1.07
6652384--6652455	21	3.4	21	84	9	85	59	0	2	37	1.12
6654030--6654089	9	6.4	9	76	16	52	31	1	0	66	1.01
6654264--6654288	2	12.5	2	100	0	50	52	0	0	48	1.00
6655537--6655572	19	1.9	19	94	5	65	30	5	0	63	1.17
6657583--6657642	20	3.0	21	78	7	61	66	5	0	28	1.12
6658188--6658251	25	2.5	25	80	7	67	48	0	1	50	1.10
6658272--6658356	34	2.5	35	78	5	93	43	0	0	56	0.99
6658292--6658321	16	1.9	15	93	6	51	36	0	0	63	0.95
6658272--6658325	17	3.2	17	76	15	58	38	0	0	61	0.96
6658371--6658462	26	3.5	26	77	10	91	53	0	1	45	1.07
6660540--6660590	20	2.6	20	81	3	59	56	1	7	33	1.39
6661026--6661072	22	2.0	22	84	8	58	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6662113--6662167	10	5.3	10	79	16	67	34	0	1	63	1.05
6662113--6662166	20	2.6	20	83	16	74	35	0	1	62	1.06
6666070--6666123	25	2.2	24	83	3	63	55	1	0	42	1.10
6666389--6666435	2	23.5	2	91	0	76	0	4	51	44	1.21
6671220--6671254	14	2.5	14	90	0	52	51	0	0	48	1.00
6671942--6671990	19	2.5	20	80	16	57	20	0	6	73	1.04
6674662--6674716	16	3.4	16	81	18	62	30	0	0	69	0.89
6675086--6675245	32	5.4	29	71	22	100	55	1	0	41	1.15
6675145--6675245	28	3.5	29	75	16	102	54	1	0	42	1.18
6675209--6675256	18	2.6	18	78	18	53	56	0	0	43	0.99
6675244--6675281	14	2.5	15	83	16	51	65	0	0	34	0.93
6676045--6676078	17	2.0	17	100	0	68	23	11	29	35	1.90
6685988--6686034	21	2.2	21	85	11	60	76	8	8	6	1.15
6686277--6686302	9	2.9	9	100	0	52	92	7	0	0	0.39
6687358--6688096	27	27.0	27	90	1	1127	23	33	14	29	1.94
6687358--6688096	82	9.0	81	90	2	1129	23	33	14	29	1.94
6688079--6688589	32	16.0	32	94	0	844	30	35	18	15	1.92
6689146--6689197	20	2.6	20	84	0	68	34	13	11	40	1.81
6690114--6690162	23	2.1	23	100	0	98	16	8	8	67	1.40
6690108--6690162	23	2.5	21	88	11	92	18	10	9	61	1.54
6697417--6697460	12	3.3	12	80	20	52	61	2	0	36	1.09
6697398--6697477	27	2.9	29	76	9	78	57	3	3	35	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6699729--6699787	29	2.1	29	87	3	84	54	13	11	20	1.70
6699951--6700202	60	4.2	60	77	6	224	47	18	15	18	1.82
6699944--6700166	120	1.9	120	82	3	288	46	20	15	17	1.84
6700153--6700210	30	1.9	30	86	6	82	55	10	10	24	1.65
6701529--6701572	17	2.6	17	81	0	61	63	4	2	29	1.26
6701592--6701648	19	2.9	19	73	14	53	59	0	1	38	1.08
6701885--6701926	2	21.0	2	100	0	84	50	0	0	50	1.00
6702019--6702064	18	2.6	18	92	0	74	8	4	4	82	0.93
6702410--6702464	19	3.1	19	85	10	73	69	3	0	27	1.05
6702811--6702848	20	2.0	20	89	5	60	36	0	0	63	0.95
6703234--6703276	3	14.3	3	90	0	68	62	0	0	37	0.95
6703231--6703280	12	4.2	12	87	2	66	60	0	0	40	0.97
6703444--6703486	20	2.2	20	87	8	61	41	4	9	44	1.57
6704178--6704207	15	1.9	16	93	6	53	73	0	0	26	0.84
6707645--6707700	29	2.0	28	86	10	78	35	7	10	46	1.66
6708761--6708799	2	19.5	2	100	0	78	48	0	0	51	1.00
6708977--6709125	79	1.9	80	84	4	203	39	18	10	30	1.85
6714137--6714182	2	23.0	2	90	0	74	47	2	2	47	1.26
6714315--6714370	11	4.8	11	75	18	51	64	0	0	35	0.94
6714315--6714390	29	2.5	32	83	12	97	61	0	0	38	0.96
6714314--6714388	38	2.1	35	87	7	105	61	0	0	38	0.96
6716014--6716055	22	2.0	22	85	4	59	38	2	7	52	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6716624--6716740	57	2.0	57	82	8	139	52	4	7	35	1.50
6716938--6716975	15	2.4	17	86	13	62	50	0	5	44	1.24
6716958--6717007	22	2.3	22	86	3	66	50	4	6	40	1.46
6718647--6718718	20	3.8	19	74	17	60	54	1	1	43	1.17
6718738--6718779	20	2.1	20	100	0	84	47	23	4	23	1.70
6720753--6720779	2	13.5	2	100	0	54	51	0	0	48	1.00
6722219--6722264	24	1.9	24	86	8	67	34	0	2	63	1.07
6723067--6723133	19	3.5	19	71	13	57	40	0	0	59	0.97
6723067--6723119	28	1.9	27	85	11	72	41	0	0	58	0.98
6727300--6727334	2	17.5	2	100	0	70	0	48	0	51	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   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52