genome.fa.s25.2.7.7.80.10.50.1000.19.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  19  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)
3442573--3442622	15	3.4	15	72	5	57	32	0	2	66	1.03
3442621--3442661	18	2.3	18	87	8	57	68	0	0	31	0.90
3442622--3442686	10	6.9	10	70	29	54	61	0	0	38	0.96
3442866--3442917	14	3.6	14	82	5	68	65	0	0	34	0.93
3442856--3442918	29	2.1	30	88	8	94	60	0	0	39	0.97
3443375--3443413	18	2.2	18	85	0	51	35	0	2	61	1.10
3444867--3444979	55	2.1	55	96	0	208	50	7	7	33	1.61
3448237--3448276	2	20.0	2	100	0	80	50	0	0	50	1.00
3448897--3448944	20	2.5	19	80	12	53	43	0	0	56	0.99
3450099--3450123	5	5.0	5	100	0	50	0	20	0	80	0.72
3450626--3450672	2	23.5	2	86	0	67	46	2	0	51	1.13
3451761--3451790	6	4.8	6	95	4	51	53	0	0	46	1.00
3451865--3451913	20	2.4	20	86	3	62	59	2	0	38	1.09
3452967--3453003	16	2.2	17	95	4	67	51	8	0	40	1.32
3457107--3457148	2	21.0	2	95	0	75	50	2	47	0	1.14
3466803--3466841	16	2.4	16	86	4	51	43	10	0	46	1.37
3467450--3467511	4	15.8	4	86	9	76	75	1	0	22	0.88
3470804--3470874	6	11.8	6	96	0	124	47	15	2	33	1.60
3476928--3476968	20	2.1	20	86	4	57	21	7	7	63	1.45
3477170--3477227	21	2.6	22	81	13	66	31	1	0	67	1.01
3477190--3477225	10	3.5	10	85	7	54	25	0	0	75	0.81
3477170--3477230	29	2.0	32	81	18	76	29	1	0	68	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3480909--3480952	21	2.1	21	83	8	54	54	0	0	45	0.99
3480932--3481000	22	3.1	21	76	12	66	53	0	0	46	1.00
3481493--3481548	29	2.0	28	89	3	85	35	3	0	60	1.14
3481646--3481724	25	2.9	30	71	21	82	59	0	1	39	1.06
3492281--3492323	12	3.6	12	87	0	50	2	53	4	39	1.34
3493393--3493539	18	8.3	18	69	20	80	40	0	1	58	1.07
3493393--3493539	29	4.9	29	69	22	90	40	0	1	58	1.07
3493413--3493535	65	1.9	65	85	11	171	43	0	0	56	1.05
3493406--3493539	8	14.3	10	69	16	67	41	0	0	58	1.03
3493498--3493569	27	2.7	26	76	16	76	43	1	1	54	1.17
3493417--3493562	64	2.2	66	79	11	158	42	0	1	55	1.13
3494089--3494139	19	2.9	18	82	8	61	37	3	0	58	1.16
3494154--3494188	18	1.9	18	88	11	54	37	2	0	60	1.12
3495369--3495435	22	3.1	21	76	2	62	56	1	2	38	1.24
3507057--3507090	2	17.0	2	100	0	68	0	50	0	50	1.00
3507643--3507743	51	1.9	53	81	15	122	54	1	0	43	1.11
3507910--3507955	19	2.4	19	82	10	58	50	0	2	47	1.13
3508073--3508097	13	1.9	13	100	0	50	24	0	12	64	1.27
3508380--3508414	18	1.9	18	88	0	52	34	0	14	51	1.42
3508508--3508541	14	2.4	14	95	0	59	44	5	0	50	1.26
3509679--3509706	3	9.3	3	100	0	56	67	0	0	32	0.91
3510699--3510732	15	2.3	15	94	0	59	47	0	2	50	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3511177--3511229	4	14.2	4	78	11	51	79	0	20	0	0.74
3511183--3511243	25	2.5	24	78	5	79	83	0	16	0	0.64
3511177--3511242	8	8.1	8	76	15	55	81	0	18	0	0.68
3511177--3511243	34	2.0	34	85	8	93	82	0	17	0	0.68
3511253--3511343	31	2.9	31	95	1	155	32	0	5	61	1.19
3512278--3512390	58	1.9	59	83	1	147	30	10	7	51	1.63
3512520--3512563	10	4.3	10	82	5	52	81	0	15	2	0.78
3513536--3513625	30	3.3	27	71	17	78	42	0	0	57	0.98
3513566--3513635	14	4.7	15	72	21	58	44	0	0	55	0.99
3515177--3515219	2	21.5	2	95	0	77	53	0	0	46	1.00
3526891--3526931	17	2.7	16	78	21	52	36	0	56	7	1.27
3532540--3532576	18	2.2	17	90	9	58	67	0	0	32	0.91
3532547--3532600	26	2.1	26	85	0	72	66	0	5	27	1.13
3533356--3533448	30	3.1	29	80	13	100	39	1	1	58	1.13
3533371--3533427	28	2.1	29	87	9	84	42	0	0	57	0.98
3533369--3533461	29	3.3	26	79	16	96	45	1	1	52	1.15
3533369--3533461	28	3.3	26	77	14	71	45	1	1	52	1.15
3533371--3533451	29	2.8	28	83	10	101	40	1	1	56	1.15
3533659--3533729	29	2.5	27	72	19	63	53	1	0	45	1.09
3533677--3533754	28	2.9	26	78	20	81	51	1	0	47	1.09
3533713--3533790	30	2.6	30	78	15	81	53	0	1	44	1.08
3534967--3534997	16	1.9	16	93	0	53	51	9	16	22	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3535570--3535624	23	2.3	25	78	12	62	52	3	0	43	1.18
3535673--3535699	13	2.1	13	100	0	54	51	0	0	48	1.00
3537876--3537925	18	2.7	18	78	3	55	50	4	2	44	1.32
3537921--3537951	14	2.2	14	100	0	62	29	0	0	70	0.87
3538190--3538214	13	1.9	13	100	0	50	0	4	0	96	0.24
3538362--3538398	17	2.2	17	90	9	58	0	18	0	81	0.70
3538362--3538402	6	7.0	6	89	10	59	0	19	0	80	0.71
3539017--3539044	13	2.2	13	100	0	56	53	7	7	32	1.55
3545864--3545938	16	4.4	16	68	17	53	45	0	0	54	0.99
3545879--3545955	32	2.4	31	79	12	84	42	1	1	54	1.16
3546633--3546662	16	1.9	15	93	6	51	50	10	0	40	1.36
3550270--3550302	12	2.6	13	85	9	50	33	0	3	63	1.10
3550257--3550299	19	2.2	20	80	12	54	27	0	4	67	1.10
3550444--3550479	8	4.2	9	89	10	58	80	0	0	19	0.71
3550444--3550479	17	2.1	17	94	0	63	80	0	0	19	0.71
3551254--3551295	18	2.3	18	84	15	52	35	2	0	61	1.09
3551325--3551366	2	21.0	2	100	0	84	50	0	0	50	1.00
3551724--3551778	24	2.5	22	88	8	76	50	1	0	47	1.11
3553290--3553332	3	14.3	3	100	0	86	67	0	0	32	0.91
3555732--3555866	65	2.1	65	98	1	263	25	16	8	49	1.73
3556131--3556165	2	18.5	2	88	11	56	48	0	0	51	1.00
3558813--3558853	10	4.1	10	81	12	57	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3558809--3558900	19	4.9	19	71	20	70	59	0	1	39	1.04
3558814--3558900	16	5.8	16	67	26	57	59	0	1	39	1.05
3558809--3558942	27	4.9	27	73	16	87	56	0	0	42	1.04
3558817--3558944	19	7.4	19	71	17	59	57	0	0	42	1.04
3562649--3562694	21	2.2	21	84	0	56	41	4	2	52	1.33
3562790--3562841	11	4.6	11	75	11	52	57	0	0	42	0.98
3564769--3564793	13	1.9	13	100	0	50	92	8	0	0	0.40
3565210--3565279	33	2.2	33	87	5	99	45	2	0	51	1.16
3565264--3565317	6	9.2	6	73	18	51	35	1	1	61	1.18
3565263--3565340	38	2.0	42	85	10	110	35	2	1	60	1.19
3565582--3565622	22	1.9	22	90	5	66	51	0	0	48	1.00
3569974--3570035	32	1.9	33	86	3	90	48	3	1	46	1.28
3570166--3570228	27	2.4	26	81	5	72	53	0	0	46	1.00
3570436--3570461	9	2.9	9	100	0	52	30	0	34	34	1.58
3572216--3572285	22	3.1	22	74	13	70	57	0	2	40	1.14
3573289--3573326	17	2.2	18	85	4	51	71	0	0	28	0.87
3573480--3573545	26	2.6	27	75	15	70	40	0	0	59	0.98
3573483--3573529	15	3.0	15	78	15	51	34	0	0	65	0.93
3573659--3573730	24	3.3	22	83	11	94	47	0	0	52	1.00
3573659--3573730	22	3.3	23	85	11	98	47	0	0	52	1.00
3573907--3573956	6	8.3	6	82	8	57	80	4	16	0	0.87
3585535--3585612	36	2.1	37	81	11	90	46	0	1	52	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3590764--3590816	13	4.2	13	73	7	56	28	1	0	69	0.99
3593129--3593153	11	2.3	11	100	0	50	92	8	0	0	0.40
3598240--3598512	100	2.8	100	84	7	311	29	16	4	49	1.64
3598372--3598430	30	2.0	30	86	6	84	25	16	0	57	1.39
3598339--3598512	88	2.0	88	90	2	278	31	14	3	50	1.60
3598674--3598767	20	4.8	19	69	14	57	51	2	0	46	1.13
3598668--3598692	7	3.6	7	100	0	50	60	0	0	40	0.97
3598840--3598872	17	2.0	17	94	5	59	48	0	0	51	1.00
3604616--3604660	23	2.0	23	90	0	72	53	0	2	44	1.13
3604842--3604900	27	2.1	28	87	3	84	30	16	13	38	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   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56