genome.fa.s8.2.7.7.80.10.50.1000.23.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: 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  23  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)
3756500--3756533	17	1.9	18	88	5	52	29	0	2	67	1.05
3757129--3757166	15	2.5	15	83	12	51	52	2	0	44	1.14
3757318--3757398	32	2.5	33	82	7	87	40	4	1	53	1.31
3758820--3758850	2	15.5	2	100	0	62	51	0	48	0	1.00
3759504--3759549	24	1.9	24	81	0	56	54	2	0	43	1.12
3761811--3761860	18	2.8	18	85	11	59	64	0	0	36	0.94
3762080--3762111	16	2.0	16	93	0	55	28	6	0	65	1.16
3762339--3762367	2	14.5	2	100	0	58	51	0	0	48	1.00
3762937--3762978	18	2.3	18	88	8	59	28	7	0	64	1.20
3763639--3763671	14	2.3	15	94	5	59	45	0	0	54	0.99
3763639--3763682	16	2.9	14	83	12	52	40	0	0	59	0.98
3763639--3763682	15	3.0	16	81	15	51	40	0	0	59	0.98
3763674--3763729	24	2.5	22	86	13	71	39	0	1	58	1.08
3765509--3765792	101	2.8	101	89	0	417	30	18	19	30	1.96
3765509--3765794	50	5.7	51	89	2	407	30	18	19	31	1.96
3770187--3770520	50	6.6	50	94	0	542	28	19	20	30	1.97
3778254--3778292	18	2.2	18	95	0	69	28	23	17	30	1.97
3779816--3779844	12	2.3	13	94	5	51	0	20	0	79	0.74
3780123--3780243	4	29.2	4	70	18	61	46	19	3	31	1.66
3780162--3780231	10	7.4	10	71	20	53	45	21	4	28	1.70
3780121--3780235	14	8.4	14	73	5	74	46	19	3	31	1.66
3780127--3780259	46	2.9	46	77	0	140	46	22	3	27	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3795237--3795371	64	2.1	64	97	1	254	32	28	10	28	1.90
3807000--3807118	60	2.0	60	91	3	195	29	20	21	28	1.98
3808438--3808464	2	13.5	2	100	0	54	48	0	0	51	1.00
3813410--3813446	2	18.5	2	94	0	65	54	0	0	45	1.00
3818081--3818114	15	2.3	15	89	0	50	67	0	26	5	1.13
3820569--3820593	3	8.3	3	100	0	50	0	36	0	64	0.94
3820980--3821018	2	19.5	2	100	0	78	51	0	0	48	1.00
3821426--3821453	2	14.0	2	100	0	56	50	0	0	50	1.00
3822700--3822789	6	15.0	6	88	0	72	34	42	12	11	1.78
3822700--3822789	18	5.0	18	79	0	81	34	42	12	11	1.78
3826422--3826507	42	2.0	42	97	0	163	41	9	12	36	1.75
3842285--3842336	27	1.9	27	84	7	70	57	0	0	42	0.98
3842862--3842901	2	20.0	2	100	0	80	50	0	0	50	1.00
3843401--3843434	2	17.0	2	100	0	68	50	0	0	50	1.00
3848512--3848832	58	5.5	58	85	4	398	14	18	33	33	1.91
3855330--3855369	20	2.0	21	85	5	55	40	5	2	52	1.37
3859391--3859435	23	2.0	23	86	0	63	31	2	11	55	1.47
3862749--3862781	7	4.9	7	85	7	50	42	0	3	54	1.15
3862749--3862792	14	3.1	14	83	12	54	43	0	4	52	1.22
3864329--3864366	2	19.0	2	100	0	76	50	0	0	50	1.00
3865748--3865773	2	13.0	2	100	0	52	50	0	0	50	1.00
3866840--3866899	30	2.0	29	81	9	68	55	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3873048--3873094	2	23.5	2	100	0	94	48	0	0	51	1.00
3880732--3880763	14	2.2	15	94	5	57	50	0	0	50	1.00
3880741--3880784	22	2.1	21	88	12	65	56	0	0	43	0.99
3884677--3884716	21	2.0	21	85	9	57	37	2	0	60	1.11
3886834--3886869	5	7.2	5	93	0	63	22	0	0	77	0.76
3887296--3887330	2	17.5	2	100	0	70	51	0	0	48	1.00
3888495--3888526	4	7.8	4	96	3	55	25	0	3	71	1.00
3892955--3893002	16	3.0	16	85	14	64	60	0	2	37	1.09
3893232--3893275	20	2.3	19	84	4	52	25	2	4	68	1.20
3893295--3893331	18	2.0	19	89	5	58	51	0	2	45	1.15
3893393--3893451	23	2.5	24	81	8	59	52	3	0	44	1.17
3896237--3896298	32	1.9	32	87	6	90	45	3	0	51	1.17
3917250--3917283	3	11.3	3	100	0	68	35	0	32	32	1.58
3917770--3917797	2	14.0	2	100	0	56	50	0	0	50	1.00
3918102--3918143	22	2.0	21	86	13	59	42	0	0	57	0.99
3918077--3918143	24	2.9	24	78	10	70	43	0	0	56	0.99
3918600--3918626	2	13.5	2	100	0	54	48	0	0	51	1.00
3918731--3918883	21	7.4	21	71	10	100	51	6	3	38	1.44
3918751--3918969	42	5.2	42	72	17	141	50	8	4	37	1.52
3918703--3918887	21	8.9	21	72	7	83	52	6	2	38	1.42
3918826--3918933	43	2.4	43	80	10	103	51	10	3	34	1.53
3918931--3918976	20	2.5	18	82	10	58	47	4	6	41	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3923670--3923703	14	2.4	14	90	0	50	14	0	5	79	0.91
3924369--3924406	8	4.8	8	86	0	58	0	36	0	63	0.95
3924366--3924405	10	4.0	10	83	0	53	0	37	0	62	0.95
3924429--3924474	3	15.3	3	100	0	92	32	0	0	67	0.91
3925906--3925937	3	10.7	3	93	0	55	65	3	0	31	1.08
3928200--3928571	198	1.9	198	97	0	708	39	18	8	33	1.81
3930454--3930486	6	5.5	6	89	10	50	84	3	0	12	0.72
3930454--3930487	17	1.9	17	88	5	50	82	2	0	14	0.79
3937794--3937836	16	2.8	16	79	6	54	53	0	0	46	1.00
3937808--3937927	38	3.2	37	70	19	115	51	1	0	45	1.16
3937789--3937940	73	2.1	71	86	4	207	51	1	0	45	1.17
3941377--3941409	2	16.5	2	100	0	66	51	48	0	0	1.00
3943669--3943751	32	2.6	32	98	0	157	60	8	10	20	1.56
3944978--3945010	16	2.1	16	100	0	66	54	6	15	24	1.63
3948286--3948336	20	2.7	18	82	14	59	68	0	0	31	0.90
3956414--3956490	37	2.1	37	87	2	111	44	10	18	27	1.82
3962427--3962456	2	15.0	2	92	0	51	53	0	0	46	1.00
3962721--3962765	5	9.6	5	76	13	51	33	0	2	64	1.06
3962701--3962764	27	2.4	27	78	0	65	42	0	1	56	1.09
3962713--3962767	27	2.0	27	85	0	74	38	0	1	60	1.08
3966719--3966751	13	2.8	12	90	9	50	0	9	0	90	0.44
3967274--3967311	20	1.9	20	100	0	76	18	23	10	47	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3975778--3975812	14	2.5	13	86	13	52	31	0	0	68	0.90
3975779--3975804	7	3.7	7	100	0	52	26	0	0	73	0.84
3976543--3976577	17	2.1	17	89	5	54	48	0	0	51	1.00
3976550--3976588	17	2.3	17	81	0	51	48	0	0	51	1.00
3976541--3976599	22	2.9	21	76	19	54	47	0	0	52	1.00
3976871--3976950	30	2.7	30	79	7	85	50	2	2	45	1.28
3983921--3983957	11	3.0	13	76	15	51	48	0	0	51	1.00
3991272--3991312	19	2.2	19	86	8	57	43	2	4	48	1.37
3994118--3994147	15	2.1	15	93	6	53	36	16	6	40	1.75
3994232--3994271	21	1.9	21	89	0	62	52	0	0	47	1.00
3996591--3996619	2	14.5	2	100	0	58	0	0	48	51	1.00
3999142--3999223	6	12.7	7	71	23	56	52	1	0	46	1.08
3999139--3999222	25	3.3	26	80	12	95	52	1	0	46	1.08
3999777--3999814	19	2.0	19	94	0	67	65	0	0	34	0.93
3999917--3999955	2	20.0	2	94	5	71	48	0	0	51	1.00
4000114--4000173	28	2.1	28	84	6	77	46	0	0	53	1.00
4000122--4000174	28	1.9	27	88	3	79	43	0	0	56	0.99
4000280--4000317	16	2.3	17	86	9	60	55	0	0	44	0.99
4000870--4000930	32	1.9	33	86	6	90	55	1	0	42	1.09
4000868--4000925	17	3.6	16	70	27	50	58	1	0	39	1.08
4000898--4000982	26	3.1	27	73	19	70	57	1	0	41	1.06
4001226--4001258	12	2.5	14	90	9	52	21	6	6	66	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4001514--4001561	18	2.6	19	80	16	64	50	2	0	47	1.12
4006329--4006363	2	17.5	2	100	0	70	51	0	0	48	1.00
4010592--4010647	19	3.0	19	79	7	62	35	0	0	64	0.94
4010664--4010770	37	2.9	37	73	14	96	42	0	1	56	1.10
4010663--4010850	26	7.2	26	64	20	70	40	0	1	56	1.13
4010692--4010736	19	2.4	19	81	3	56	40	0	2	57	1.11
4010671--4010743	23	3.4	20	74	24	60	42	0	1	56	1.08
4010712--4010840	56	2.3	53	79	18	138	41	0	2	55	1.18
4010805--4010852	25	2.0	24	87	4	69	39	0	2	58	1.10
4011189--4011213	13	1.9	13	100	0	50	44	16	0	40	1.47

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