genome.fa.s3.2.7.7.80.10.50.1000.23.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  23  of  32  ( 3795 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)
3860463--3860497	11	3.2	11	87	0	52	60	0	0	40	0.97
3860457--3860517	26	2.3	27	76	20	67	62	0	0	37	0.96
3860477--3860515	17	2.4	16	82	4	51	66	0	0	33	0.92
3860938--3860990	26	2.0	27	88	3	81	56	0	5	37	1.23
3864963--3865065	20	5.2	20	67	19	54	59	0	0	39	1.04
3864977--3865062	32	2.6	33	85	7	120	58	0	0	41	0.98
3865002--3865058	16	3.4	17	77	18	66	56	0	0	43	0.99
3868920--3868949	2	15.0	2	100	0	60	50	0	0	50	1.00
3873797--3873829	2	16.5	2	93	0	57	45	0	3	51	1.16
3878490--3878543	15	3.8	15	76	11	51	53	0	0	46	1.00
3878471--3878537	29	2.3	29	82	2	82	56	0	1	41	1.08
3878502--3878550	20	2.4	19	81	18	55	53	2	0	44	1.12
3880849--3880886	20	1.9	20	84	10	51	26	10	21	42	1.85
3887733--3887785	27	2.0	27	89	10	83	54	0	5	39	1.24
3891766--3891850	32	2.6	33	85	9	120	58	0	0	41	0.98
3891771--3891850	8	9.8	8	70	23	51	58	0	0	41	0.98
3891779--3891846	16	3.9	17	76	20	70	55	0	0	44	0.99
3892347--3892378	14	2.2	15	94	5	57	56	6	0	37	1.25
3895693--3895746	2	27.0	2	96	0	99	48	1	0	50	1.11
3900595--3900627	2	16.5	2	93	0	57	45	0	3	51	1.16
3907544--3907595	21	2.5	20	73	14	52	55	0	0	44	0.99
3907583--3907645	28	2.3	27	76	10	67	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3907745--3907863	59	2.0	59	91	0	193	31	10	22	34	1.89
3911324--3911372	18	2.7	18	84	9	64	57	0	0	42	0.99
3911417--3911453	11	3.1	13	81	18	53	35	0	0	64	0.94
3911394--3911506	53	2.1	53	85	3	156	43	3	0	52	1.24
3913604--3913666	27	2.4	27	76	10	67	57	1	0	41	1.08
3914852--3914921	17	4.2	17	73	20	60	55	0	1	42	1.08
3922992--3923025	2	17.0	2	100	0	68	50	0	0	50	1.00
3926215--3926249	16	2.1	18	89	10	56	0	5	5	88	0.63
3929231--3929313	14	5.5	15	72	18	57	55	0	0	44	0.99
3929231--3929313	21	3.3	26	74	22	79	55	0	0	44	0.99
3929271--3929328	6	9.8	6	71	17	50	63	0	0	36	0.94
3929577--3929617	21	1.9	21	85	14	57	29	4	2	63	1.28
3939621--3939996	118	3.2	115	86	4	520	17	15	31	34	1.92
3939606--3940032	58	7.3	58	78	6	405	17	17	31	33	1.93
3939673--3939997	176	1.8	177	83	2	429	18	16	31	33	1.93
3944889--3944953	34	1.9	34	83	0	85	29	21	29	20	1.98
3945474--3945500	14	1.9	14	100	0	54	81	0	0	18	0.69
3974655--3974679	13	1.9	13	100	0	50	72	0	8	20	1.10
3975127--3975162	3	12.0	3	100	0	72	66	0	0	33	0.92
3976193--3976245	17	3.2	16	73	7	52	39	0	0	60	0.97
3976238--3976307	29	2.3	31	76	16	76	52	1	0	45	1.09
3976244--3976289	17	2.6	17	86	3	65	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3976241--3976344	23	5.0	22	69	23	75	52	0	0	46	1.07
3976634--3976663	2	15.0	2	100	0	60	50	0	0	50	1.00
3978813--3978859	21	2.2	22	85	11	62	59	2	4	34	1.29
3981449--3981497	21	2.3	21	92	0	80	55	0	8	36	1.30
3981940--3981965	2	13.0	2	100	0	52	50	0	0	50	1.00
3983520--3983600	22	3.7	22	73	14	60	49	0	1	49	1.08
3983552--3983611	31	1.9	31	86	6	86	46	0	1	51	1.10
3985873--3985916	3	14.7	3	80	0	52	34	34	22	9	1.86
3985876--3985920	6	7.5	6	97	0	72	33	33	22	11	1.89
3987268--3987321	27	2.0	27	100	0	108	29	22	18	29	1.97
3987340--3987377	2	19.0	2	94	0	67	50	0	2	47	1.15
3989836--3989863	2	14.0	2	100	0	56	50	0	0	50	1.00
3990574--3990628	15	3.6	15	86	11	76	43	0	1	54	1.10
3990574--3990645	15	4.6	16	79	17	64	44	0	1	54	1.08
3990597--3990650	9	6.2	9	79	20	62	42	0	0	57	0.98
3990597--3990650	25	2.1	26	89	6	83	42	0	0	57	0.98
3990622--3990710	16	5.6	16	77	6	74	39	3	6	50	1.45
3990775--3990834	21	2.8	21	80	5	59	38	6	10	45	1.64
3991556--3991611	16	3.5	16	70	0	58	30	12	14	42	1.82
3992089--3992128	2	20.0	2	100	0	80	50	0	0	50	1.00
3992938--3992968	6	5.2	6	96	0	53	64	0	0	35	0.94
3993424--3993475	22	2.4	21	87	9	70	42	0	5	51	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3995651--3995694	20	2.2	20	95	0	79	18	36	13	31	1.90
4000600--4000633	18	1.9	18	88	5	52	29	14	0	55	1.40
4003781--4003994	34	6.4	34	83	3	245	27	7	24	41	1.81
4003781--4003996	67	3.2	66	83	3	254	26	6	25	41	1.80
4005393--4005435	20	2.1	21	86	4	61	51	0	0	48	1.00
4005801--4005851	19	3.0	17	78	15	52	39	0	0	60	0.97
4005853--4005896	7	6.0	7	79	10	52	61	2	0	36	1.09
4007027--4007063	2	18.5	2	100	0	74	48	0	0	51	1.00
4008601--4008669	33	2.1	33	97	0	129	13	36	17	33	1.88
4010878--4010915	6	6.5	6	90	6	51	89	0	10	0	0.49
4010877--4010916	11	4.0	10	87	9	55	87	0	12	0	0.54
4011941--4012002	20	3.1	20	76	15	65	37	1	0	61	1.06
4011946--4011995	22	2.2	24	82	7	59	36	2	0	62	1.07
4012042--4012093	15	3.4	15	77	17	54	69	3	0	26	1.06
4015818--4015854	18	2.1	18	100	0	74	43	21	16	18	1.88
4016605--4016643	2	19.5	2	100	0	78	51	0	48	0	1.00
4022370--4022403	6	5.7	6	96	0	59	38	0	0	61	0.96
4027142--4027180	20	2.1	18	85	9	51	0	17	5	76	0.96
4030605--4030647	21	2.1	21	87	8	63	44	2	0	53	1.13
4031053--4031082	2	15.0	2	92	0	51	50	3	0	46	1.18
4031194--4031246	23	2.2	25	86	6	74	64	0	1	33	1.05
4032280--4032324	2	22.5	2	100	0	90	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4032324--4032352	2	15.0	2	92	7	51	48	0	0	51	1.00
4037140--4037196	24	2.4	23	80	11	62	57	0	3	38	1.16
4039303--4039337	16	2.1	17	89	5	54	60	0	0	40	0.97
4039380--4039435	15	3.8	15	72	11	53	33	0	0	66	0.92
4039619--4039668	22	2.3	21	80	10	57	70	2	12	16	1.26
4050669--4050717	2	24.5	2	100	0	98	51	0	0	48	1.00
4055232--4055268	3	12.3	3	94	0	65	67	0	32	0	0.91
4055762--4055808	24	2.0	24	86	0	67	42	2	0	55	1.12
4056567--4056591	7	3.6	7	100	0	50	0	0	16	84	0.63
4058028--4058068	17	2.3	19	83	8	50	51	0	0	48	1.00
4063136--4063194	27	2.2	27	81	6	66	40	28	6	23	1.80
4064101--4064142	20	2.1	20	95	0	75	21	16	23	38	1.93
4064257--4064303	12	3.7	13	83	11	53	42	2	2	53	1.25
4064272--4064308	12	3.2	12	88	11	51	45	0	0	54	1.00
4067095--4067141	2	23.5	2	100	0	94	51	0	0	48	1.00
4072303--4072332	2	15.0	2	100	0	60	50	0	0	50	1.00
4079093--4079134	20	2.0	21	86	4	59	45	0	0	54	0.99
4079092--4079143	21	2.5	21	81	9	61	44	0	0	55	0.99
4079106--4079146	17	2.3	18	87	4	57	48	0	0	51	1.00
4081751--4081784	4	8.2	4	87	6	50	20	0	0	79	0.73
4082143--4082183	21	1.9	22	85	14	59	39	2	0	58	1.11
4083064--4083090	7	3.9	7	100	0	54	14	29	29	25	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4093695--4093736	19	2.3	19	92	8	70	40	0	2	57	1.12
4094340--4094387	24	2.0	24	83	0	60	39	10	2	47	1.49
4095642--4095682	22	1.9	22	85	5	57	31	24	7	36	1.83
4097201--4097241	21	1.9	21	85	5	55	43	2	2	51	1.28
4098150--4098178	13	2.1	14	93	6	51	51	0	0	48	1.00
4098167--4098205	19	2.0	20	85	5	53	41	0	0	58	0.98
4098707--4098793	23	3.9	22	77	14	72	62	0	0	37	0.96
4098720--4098805	10	8.2	10	74	24	63	62	0	0	37	0.95
4098701--4098805	22	5.0	20	72	21	74	62	0	0	36	1.02
4098681--4098753	37	2.0	37	81	10	87	60	1	1	36	1.14

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