genome.fa.s2.2.7.7.80.10.50.1000.24.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  24  of  38  ( 4457 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)
3708727--3708773	21	2.3	20	85	7	67	23	14	19	42	1.88
3714362--3714396	14	2.5	14	90	0	52	48	11	8	31	1.69
3714471--3714536	28	2.4	27	90	5	98	25	22	24	27	2.00
3714757--3714936	32	5.6	32	85	5	222	30	30	18	20	1.97
3714757--3714931	65	2.7	63	87	3	235	30	30	17	20	1.96
3714757--3714955	63	3.1	63	83	5	188	29	31	17	21	1.96
3715058--3715159	52	2.0	52	88	0	150	25	22	16	35	1.95
3720320--3720359	21	1.9	21	89	0	62	45	0	0	55	0.99
3721496--3721944	152	2.9	152	81	6	489	49	8	7	34	1.61
3724146--3724250	31	3.5	30	79	10	115	24	28	16	30	1.96
3724152--3724236	29	2.9	28	82	8	107	25	28	18	27	1.98
3724213--3724604	60	6.4	60	75	13	245	21	30	12	34	1.91
3724265--3724633	33	11.8	32	79	9	281	21	31	12	34	1.91
3724243--3724408	28	5.8	28	77	10	131	24	33	13	28	1.93
3724353--3724633	94	2.9	94	80	7	291	20	30	12	35	1.91
3724265--3724604	67	5.5	64	77	11	284	21	31	12	35	1.90
3724474--3724623	67	2.3	67	83	4	196	21	31	10	36	1.88
3724749--3724991	39	5.8	39	73	15	189	27	25	19	26	1.99
3724777--3724962	47	4.1	47	74	11	181	28	25	18	27	1.98
3724970--3725217	49	4.9	52	83	5	328	22	26	18	32	1.97
3724970--3725260	101	2.9	101	89	1	429	23	26	18	32	1.97
3724972--3725358	52	7.5	51	76	8	313	24	25	17	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3726050--3726116	20	3.4	19	81	8	80	32	13	11	41	1.81
3730829--3730881	20	2.7	20	85	8	72	41	16	13	28	1.86
3737046--3737084	13	3.0	13	96	0	69	30	17	15	35	1.91
3737196--3737241	21	2.2	20	81	11	58	32	19	4	43	1.71
3739655--3739680	13	2.0	13	100	0	52	38	15	15	30	1.88
3739636--3739701	33	2.0	34	87	3	98	42	16	13	27	1.86
3743110--3743139	15	2.0	15	100	0	60	26	26	6	40	1.81
3744287--3744375	31	2.9	31	80	9	94	25	30	14	29	1.95
3744355--3744597	28	8.8	28	84	5	282	26	35	12	25	1.92
3744355--3744690	83	3.9	83	83	7	347	24	34	13	27	1.92
3744360--3744697	111	3.0	110	85	6	410	23	34	12	29	1.92
3744570--3744823	33	7.8	33	81	6	286	18	30	14	36	1.90
3744377--3744759	83	4.3	94	83	8	334	22	33	12	31	1.92
3744638--3744690	27	2.0	27	92	0	88	20	35	15	28	1.93
3744570--3744823	67	3.9	66	83	7	286	18	30	14	36	1.90
3744881--3745049	52	3.3	52	80	7	193	23	26	16	34	1.95
3744878--3745038	49	3.3	49	80	8	175	22	26	17	34	1.96
3745474--3745532	32	1.9	30	83	13	75	59	10	10	20	1.58
3745814--3745839	13	2.0	13	100	0	52	30	15	15	38	1.88
3748404--3748439	13	2.8	13	95	0	63	33	16	16	33	1.92
3750522--3750552	15	2.1	15	93	0	53	12	22	16	48	1.80
3753457--3753501	21	2.1	21	88	8	65	40	20	17	22	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3755784--3755868	3	29.3	3	79	11	88	24	0	2	72	0.96
3756426--3757131	43	16.6	43	64	14	176	41	14	29	15	1.86
3756426--3757666	86	14.6	86	81	5	1089	40	14	28	15	1.87
3756795--3757447	43	15.3	42	64	17	143	40	14	28	15	1.88
3757393--3757620	42	5.4	42	69	9	140	39	16	28	15	1.90
3756472--3757671	427	2.8	427	85	3	1551	40	14	28	15	1.87
3757393--3757668	84	3.3	84	83	3	304	39	17	28	15	1.90
3757519--3757662	42	3.4	42	74	3	146	37	15	30	16	1.90
3757760--3757931	44	3.9	44	68	13	122	41	15	23	19	1.89
3758081--3758742	60	11.0	60	67	12	248	38	12	25	23	1.89
3758038--3758984	120	7.9	120	80	4	870	38	12	25	23	1.90
3758112--3758272	30	5.4	30	72	14	107	39	12	25	22	1.89
3758038--3758982	240	3.9	239	81	4	986	38	12	25	23	1.90
3758424--3758959	60	8.9	60	66	9	178	38	12	25	23	1.90
3759150--3759665	89	5.8	88	78	5	409	31	15	23	29	1.95
3761252--3761290	19	2.0	21	90	10	64	5	20	2	71	1.17
3761239--3761296	30	1.9	31	85	3	82	5	18	1	74	1.10
3761672--3761697	5	5.2	5	100	0	52	19	0	0	80	0.71
3762536--3762564	14	2.1	14	100	0	58	0	34	13	51	1.42
3764268--3764293	13	2.0	13	100	0	52	30	15	15	38	1.88
3764248--3764311	32	2.0	33	90	3	103	28	14	18	39	1.90
3764248--3764318	19	4.0	18	72	25	62	26	12	21	39	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3770569--3770649	32	2.5	32	86	9	112	32	32	16	19	1.94
3770652--3771293	52	12.2	52	73	10	396	23	25	15	35	1.94
3770652--3771292	104	6.1	104	77	7	479	24	25	15	35	1.94
3770688--3771295	156	3.8	161	76	10	448	24	25	15	34	1.95
3772128--3772176	19	2.7	19	87	6	66	18	18	10	53	1.72
3772416--3772453	18	2.1	18	85	9	51	55	23	15	5	1.61
3772467--3772652	94	1.9	97	83	6	243	45	11	25	17	1.82
3773759--3774143	154	2.5	156	81	6	431	28	24	13	33	1.93
3773726--3774224	79	6.4	80	76	7	357	27	25	13	33	1.93
3776819--3776844	13	2.0	13	100	0	52	30	15	15	38	1.88
3779372--3780173	166	4.9	163	79	10	806	29	10	8	51	1.66
3779642--3779689	19	2.5	19	100	0	96	33	16	0	50	1.46
3779509--3779843	175	1.9	174	86	1	474	30	11	7	50	1.67
3780808--3780836	11	2.7	11	94	5	51	72	0	0	27	0.85
3780713--3781072	140	2.5	141	75	10	345	36	11	10	42	1.75
3786827--3786879	20	2.6	21	75	3	54	45	11	13	30	1.78
3791684--3791737	19	2.8	19	94	2	90	35	12	20	31	1.90
3792440--3792609	75	2.3	75	87	4	261	30	18	4	46	1.68
3798589--3798703	20	5.7	20	78	4	106	30	17	13	39	1.87
3802965--3802995	16	1.9	16	93	0	53	35	9	0	54	1.33
3807476--3807531	19	2.9	19	86	2	76	39	12	17	30	1.87
3812159--3812272	32	3.6	32	85	7	144	30	30	18	20	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3812283--3812397	32	3.5	33	84	4	153	31	33	15	20	1.94
3812479--3813059	52	11.0	52	77	7	548	23	22	15	38	1.93
3812479--3813060	104	5.5	104	80	7	620	23	22	15	38	1.93
3813114--3813288	61	2.9	61	76	9	155	25	22	15	37	1.93
3813212--3813385	61	2.9	61	80	3	199	25	22	12	39	1.90
3813210--3813404	61	3.2	61	77	5	180	25	22	13	38	1.91
3814052--3814108	20	2.8	20	83	2	60	38	12	17	31	1.87
3814137--3814210	20	3.6	20	77	10	69	36	16	12	35	1.86
3815082--3815115	8	4.1	8	85	7	50	82	0	0	17	0.67
3815082--3815116	17	2.1	17	88	0	52	82	0	0	17	0.66
3817704--3817868	51	3.2	51	81	5	165	30	27	10	30	1.90
3817883--3818001	51	2.3	51	92	0	193	28	23	13	34	1.93
3817753--3818395	130	4.9	129	83	3	702	27	25	13	33	1.93
3818019--3818131	51	2.2	51	88	0	163	28	25	11	34	1.91
3818143--3818261	51	2.4	51	82	1	150	29	28	14	27	1.95
3818271--3818392	52	2.3	52	82	8	142	23	24	16	35	1.95
3820456--3820780	35	9.3	35	81	3	350	21	20	12	45	1.84
3820464--3820758	104	2.8	104	87	3	423	21	19	13	46	1.83
3820456--3820774	70	4.6	70	83	3	392	22	19	12	45	1.84
3820456--3820780	139	2.3	140	82	3	352	21	20	12	45	1.84
3822194--3822917	166	4.4	165	78	9	665	29	11	8	50	1.67
3823262--3823296	12	2.9	12	91	8	54	85	0	11	2	0.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3830543--3830616	19	3.7	19	85	8	87	28	16	18	36	1.93
3830543--3830698	20	7.7	19	72	18	86	31	16	17	34	1.92
3832425--3832463	21	1.9	20	85	15	53	35	0	10	53	1.35
3833869--3833985	52	2.3	51	91	4	191	29	17	18	33	1.95
3833869--3834005	52	2.7	52	84	5	163	31	17	18	32	1.95
3833994--3834018	13	1.9	13	100	0	50	36	16	16	32	1.90
3834081--3834105	13	1.9	13	100	0	50	32	16	16	36	1.90
3835393--3835471	20	3.7	21	75	15	72	26	13	15	44	1.84
3835458--3835496	13	3.0	13	96	0	69	30	17	15	35	1.91
3837185--3837257	20	3.6	20	81	3	101	35	13	19	31	1.91

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