genome.fa.s25.2.7.7.80.10.50.1000.27.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   53   54   55   56   

This is table  27  of  56  ( 6609 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)
4593412--4593448	2	18.5	2	100	0	74	51	0	0	48	1.00
4595585--4595888	105	2.9	105	81	3	344	43	7	10	38	1.67
4597383--4597447	21	3.1	21	78	8	62	47	0	0	52	1.00
4597398--4597452	21	2.6	22	80	5	69	50	0	0	49	1.00
4604182--4604211	2	15.0	2	100	0	60	50	0	0	50	1.00
4604486--4604518	15	2.3	15	89	5	50	51	0	0	48	1.00
4604473--4604543	33	2.1	34	82	7	83	46	1	1	50	1.18
4605593--4605659	24	2.9	23	80	12	75	52	1	1	44	1.19
4609334--4609370	2	18.5	2	100	0	74	0	48	0	51	1.00
4610504--4610551	20	2.3	22	82	13	66	58	0	0	41	0.98
4610504--4610558	20	2.8	21	81	13	64	58	0	0	41	0.98
4610505--4610577	27	2.8	26	80	10	87	61	0	1	36	1.05
4610504--4610576	16	4.6	15	79	17	69	60	0	1	38	1.06
4610764--4610821	27	2.1	27	81	6	64	39	1	3	55	1.27
4610997--4611030	1	34.0	1	93	0	59	97	0	2	0	0.19
4614445--4614473	2	14.5	2	100	0	58	51	48	0	0	1.00
4614473--4614505	2	16.5	2	100	0	66	51	0	0	48	1.00
4614722--4614746	13	1.9	13	100	0	50	60	0	0	40	0.97
4616017--4616063	23	2.0	23	84	8	60	34	2	2	61	1.20
4616840--4616877	2	19.0	2	100	0	76	50	0	0	50	1.00
4619666--4619703	15	2.4	17	83	16	55	81	0	7	10	0.87
4622566--4622616	12	3.9	12	78	16	57	43	5	11	39	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4622572--4622628	27	2.1	27	90	0	87	40	5	19	35	1.74
4626192--4626242	12	3.9	12	78	16	57	43	5	11	39	1.66
4626198--4626254	27	2.1	27	90	0	87	40	5	19	35	1.74
4630772--4630810	2	19.5	2	100	0	78	0	0	48	51	1.00
4634986--4635026	2	20.5	2	89	0	64	0	51	2	46	1.14
4636022--4636068	24	2.0	24	87	8	69	53	10	0	36	1.36
4642767--4642801	13	2.7	13	83	16	54	34	14	14	37	1.86
4644127--4644187	28	2.4	23	76	17	59	59	0	0	40	0.98
4644132--4644190	26	2.2	28	85	11	79	64	0	0	35	0.94
4644389--4644422	13	2.6	13	90	9	52	73	0	0	26	0.83
4644644--4644721	30	2.6	29	86	8	102	29	0	7	62	1.23
4644667--4644719	17	3.4	17	75	20	60	28	0	7	64	1.21
4644679--4644705	13	2.1	13	100	0	54	29	0	14	55	1.40
4644638--4644738	30	3.4	29	81	8	96	29	2	7	59	1.41
4644937--4644994	22	2.8	21	77	12	57	34	1	1	62	1.16
4645043--4645092	17	2.9	17	79	5	57	64	2	2	32	1.16
4646024--4646078	15	3.3	17	73	9	51	54	0	0	45	0.99
4649777--4649821	2	22.5	2	95	0	81	2	0	48	48	1.13
4653095--4653145	22	2.5	21	84	12	63	49	0	1	49	1.12
4653118--4653160	19	2.3	18	80	4	50	48	0	0	51	1.00
4653398--4653423	2	13.0	2	100	0	52	50	0	0	50	1.00
4662287--4662315	3	9.7	3	100	0	58	68	0	0	31	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4662407--4662453	2	23.5	2	86	0	67	46	4	2	46	1.34
4663244--4663272	14	2.0	15	93	6	51	44	0	0	55	0.99
4663941--4663980	21	1.9	21	100	0	80	20	10	27	42	1.83
4666885--4666933	20	2.4	21	79	3	55	22	6	10	61	1.50
4672530--4672577	14	3.4	14	77	5	53	52	0	2	45	1.12
4673198--4673273	29	2.6	29	82	4	80	56	1	2	39	1.21
4673236--4673273	11	3.7	11	83	16	55	63	0	0	36	0.95
4673235--4673273	19	2.1	19	90	9	62	61	0	0	38	0.96
4673544--4673614	32	2.2	32	85	5	90	70	4	11	14	1.30
4674482--4674552	35	2.0	36	88	2	108	39	7	4	49	1.49
4675329--4675380	15	3.3	15	82	12	52	63	1	0	34	1.06
4675809--4675856	23	2.1	22	84	3	60	12	8	0	79	0.94
4676543--4676598	14	4.2	13	74	17	53	62	0	0	37	0.95
4676545--4676597	26	2.0	26	89	7	81	64	0	0	35	0.94
4676521--4676597	28	2.9	28	79	16	83	62	1	1	35	1.12
4676580--4676642	29	2.2	29	82	5	74	58	1	1	38	1.17
4676581--4676641	19	3.2	19	76	0	68	57	1	1	39	1.18
4679689--4679902	117	1.8	117	96	0	401	28	14	29	28	1.95
4680190--4680236	17	2.6	18	80	6	51	44	0	4	51	1.21
4681295--4681340	20	2.3	20	88	7	67	71	4	0	23	1.03
4681331--4681378	19	2.4	21	79	6	55	60	0	10	29	1.30
4683101--4683147	14	3.5	14	85	5	53	46	4	0	48	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4684758--4684867	48	2.3	47	88	1	157	35	11	18	34	1.87
4686602--4686635	6	5.8	6	89	3	52	47	2	0	50	1.16
4686711--4686745	11	3.2	11	88	12	54	25	0	0	74	0.82
4686697--4686740	14	3.1	14	78	12	54	27	0	0	72	0.85
4686691--4686757	28	2.3	29	84	5	82	26	1	0	71	0.94
4687425--4687541	58	2.0	58	96	0	216	23	16	24	35	1.94
4687767--4687835	27	2.5	27	83	6	77	24	4	23	47	1.69
4687919--4687957	20	2.0	20	89	0	60	12	46	5	35	1.65
4692338--4692408	27	2.6	27	86	6	90	22	7	22	47	1.75
4694175--4694226	18	3.0	17	77	11	61	73	0	0	26	0.84
4694174--4694226	26	2.0	28	88	7	83	71	0	0	28	0.86
4694172--4694233	34	1.9	33	84	15	85	70	0	0	29	0.87
4699901--4699935	2	17.5	2	100	0	70	48	0	0	51	1.00
4701802--4701885	44	1.9	44	90	0	132	27	9	19	44	1.81
4701888--4701966	24	3.1	24	74	22	72	68	2	0	29	1.03
4701916--4701958	15	2.8	16	78	7	52	69	4	0	25	1.07
4701994--4702109	58	2.0	58	91	1	189	42	2	0	55	1.13
4702325--4702355	14	2.2	14	94	0	53	45	0	0	54	0.99
4703634--4703664	2	15.5	2	100	0	62	48	0	0	51	1.00
4704796--4704824	3	9.7	3	100	0	58	31	34	0	34	1.58
4705195--4705252	5	12.4	5	74	20	54	60	0	0	39	0.97
4705194--4705246	19	2.8	19	74	2	54	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4705305--4705358	19	2.9	18	78	15	65	40	1	0	57	1.09
4705504--4705533	3	10.0	3	100	0	60	66	0	0	33	0.92
4709199--4709245	22	2.1	23	88	4	69	51	0	0	48	1.00
4711388--4711417	15	2.1	15	93	6	53	36	10	6	46	1.64
4711663--4711709	6	7.8	6	97	0	85	48	17	2	31	1.58
4719515--4719559	18	2.5	18	85	10	65	48	0	0	51	1.00
4719551--4719601	22	2.3	22	78	15	61	45	0	0	54	0.99
4719518--4719588	28	2.5	28	75	13	74	49	0	0	50	1.00
4722281--4722362	32	2.6	32	78	3	103	59	0	0	40	0.97
4722772--4722821	2	25.5	2	78	11	50	44	0	4	52	1.20
4722944--4722972	2	14.5	2	100	0	58	48	0	0	51	1.00
4723767--4723804	18	2.1	19	85	5	51	63	2	0	34	1.09
4723808--4723836	9	3.3	9	90	9	51	79	0	0	20	0.74
4723775--4723851	39	2.0	40	82	12	97	61	2	0	36	1.10
4723766--4723853	39	2.1	41	78	17	94	61	2	0	36	1.09
4727240--4727280	2	20.5	2	94	0	73	48	2	0	48	1.14
4728764--4728855	48	1.9	48	84	0	121	25	21	23	29	1.99
4740139--4740185	24	2.0	24	87	8	69	44	0	0	55	0.99
4740404--4740459	19	2.9	19	81	7	60	57	0	3	39	1.16
4740479--4740537	31	2.0	31	83	12	79	37	1	8	52	1.42
4740553--4740635	39	2.2	39	82	8	107	45	2	1	50	1.22
4740708--4740741	18	1.9	18	94	5	61	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4740912--4740995	22	4.0	21	75	13	75	61	4	0	33	1.17
4740912--4740957	24	2.0	22	84	16	58	63	4	0	32	1.14
4741131--4741177	13	3.4	13	78	16	58	34	0	4	61	1.15
4741104--4741194	29	2.8	33	79	19	111	43	0	2	53	1.12
4743998--4744055	29	2.1	27	87	6	80	51	1	3	43	1.28
4751015--4751043	2	14.5	2	100	0	58	51	0	0	48	1.00
4751085--4751119	2	17.5	2	100	0	70	51	0	0	48	1.00
4758672--4758706	14	2.4	14	90	4	52	34	2	2	60	1.26
4758756--4758803	19	2.5	19	80	6	53	25	2	8	64	1.32
4763639--4763672	2	17.5	2	93	6	61	50	0	0	50	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   53   54   55   56