genome.fa.s53.2.7.7.80.10.50.1000.23.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: Scaffold53
Parameters: 2 7 7 80 10 50 1000
Length:  4419549

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   

This is table  23  of  28  ( 3325 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)
3498147--3498182	15	2.4	15	95	0	63	30	8	5	55	1.52
3505714--3506048	155	2.2	156	85	7	459	40	16	11	31	1.84
3508038--3508102	32	2.0	32	90	0	103	32	13	21	32	1.93
3508856--3508929	20	3.8	19	87	8	96	32	16	16	35	1.91
3508957--3509010	20	2.7	20	85	5	74	37	12	16	33	1.87
3510604--3510638	15	2.3	15	95	0	61	42	0	28	28	1.56
3517748--3517801	18	2.8	21	81	16	71	35	16	12	35	1.87
3517729--3517802	20	3.8	19	77	13	71	36	14	13	35	1.86
3517829--3517882	20	2.7	19	88	11	74	33	14	18	33	1.92
3518667--3519240	148	3.9	147	80	5	606	36	18	20	24	1.94
3521313--3521371	23	2.6	22	74	12	57	50	3	5	40	1.41
3526963--3527014	19	2.7	20	81	6	70	28	13	13	44	1.82
3526963--3527034	20	3.7	19	81	7	74	30	13	15	40	1.86
3527080--3527109	13	2.3	13	100	0	60	33	16	13	36	1.88
3527066--3527129	33	1.9	33	84	12	87	34	15	17	32	1.91
3527095--3527149	20	2.8	20	94	0	101	36	10	18	34	1.86
3534575--3534625	21	2.5	22	84	9	63	33	19	0	47	1.50
3536309--3536356	23	2.1	23	88	3	71	39	4	16	39	1.68
3536899--3536971	20	3.7	19	85	7	76	30	15	16	38	1.89
3536997--3537048	13	4.5	13	73	26	62	32	13	17	36	1.89
3538056--3538108	21	2.5	21	84	0	70	37	24	5	32	1.79
3540241--3540266	13	2.0	13	100	0	52	30	15	15	38	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3540221--3540284	33	2.0	32	87	3	92	28	14	18	39	1.90
3540326--3540380	20	2.7	21	83	8	69	29	16	14	40	1.88
3540400--3540440	20	2.0	20	90	0	64	29	9	21	39	1.86
3548077--3548128	20	2.7	20	90	3	79	26	13	21	38	1.90
3548170--3548224	20	2.7	21	83	8	69	29	16	14	40	1.88
3550368--3550415	21	2.3	21	92	0	78	37	22	6	33	1.80
3554793--3554938	73	2.0	73	91	0	238	30	11	15	42	1.83
3558015--3558065	25	2.0	25	100	0	102	35	19	11	33	1.88
3560131--3560174	20	2.3	18	85	11	61	50	0	0	50	1.00
3560128--3560173	19	2.3	19	88	7	65	52	0	0	47	1.00
3562625--3562678	19	2.8	20	85	2	65	38	14	14	31	1.87
3565126--3565165	13	3.1	13	85	0	62	40	15	12	32	1.84
3569172--3569196	13	1.9	13	100	0	50	36	16	16	32	1.90
3569237--3569303	19	3.8	19	75	22	83	37	17	10	34	1.85
3569259--3569283	13	1.9	13	100	0	50	32	16	16	36	1.90
3569240--3569302	32	2.0	32	96	0	117	36	19	11	33	1.87
3569893--3570180	121	2.4	121	83	7	345	36	13	24	25	1.92
3570000--3570126	67	1.9	68	86	1	184	38	11	25	24	1.89
3570205--3570272	22	3.1	22	64	26	54	32	19	23	25	1.97
3570139--3571296	49	24.5	49	81	8	1215	31	18	25	24	1.97
3570129--3571257	92	12.0	93	88	5	1234	31	17	25	25	1.97
3570139--3571256	426	2.6	422	92	2	1846	31	18	25	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3571167--3571313	52	2.9	50	86	5	197	31	17	27	23	1.97
3571309--3571438	33	3.9	33	90	0	197	22	17	31	28	1.97
3571309--3571438	66	2.0	66	95	0	233	22	17	31	28	1.97
3571444--3571725	34	8.4	34	80	11	221	35	12	32	19	1.90
3571429--3571667	34	6.9	34	83	9	240	35	12	33	18	1.88
3571653--3571776	31	4.1	31	83	5	128	32	13	29	24	1.94
3571876--3571913	16	2.3	17	86	4	51	26	5	23	44	1.74
3573062--3573107	19	2.7	18	80	19	62	0	0	19	80	0.71
3584848--3584913	33	2.0	33	82	5	80	42	12	13	31	1.81
3586464--3586488	13	1.9	13	100	0	50	32	16	16	36	1.90
3586476--3586528	20	2.6	21	84	3	72	39	15	16	28	1.89
3586581--3586606	13	2.0	13	100	0	52	30	15	15	38	1.88
3586594--3586646	20	2.7	20	100	0	106	37	22	11	28	1.89
3586561--3586626	33	2.0	32	91	2	105	36	19	12	31	1.89
3592936--3592976	22	2.0	20	86	13	57	31	21	4	41	1.74
3595246--3595270	13	1.9	13	100	0	50	32	16	16	36	1.90
3595258--3595310	20	2.6	21	84	3	72	39	15	16	28	1.89
3595363--3595388	13	2.0	13	100	0	52	30	15	15	38	1.88
3595343--3595410	33	2.1	32	91	2	109	35	19	13	32	1.90
3597615--3597645	3	10.3	3	92	0	53	29	35	0	35	1.58
3599233--3599297	33	2.0	33	85	11	89	32	16	15	35	1.91
3599327--3599382	19	2.9	19	91	2	85	35	16	17	30	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3601202--3601238	2	18.5	2	100	0	74	51	0	0	48	1.00
3602601--3602673	29	2.4	31	80	15	89	41	2	0	56	1.14
3604910--3604957	2	24.0	2	86	0	69	43	4	0	52	1.20
3608426--3608478	21	2.5	21	84	6	72	35	28	3	32	1.75
3616867--3616916	18	2.6	20	78	18	61	46	0	0	54	1.00
3616878--3616939	28	2.2	28	85	5	81	46	0	0	53	1.00
3616936--3616980	24	1.9	24	86	4	65	31	4	0	64	1.13
3616938--3617033	27	3.7	26	81	13	110	33	3	1	62	1.18
3619399--3619836	79	5.6	78	68	12	275	32	13	25	28	1.93
3619552--3619627	28	2.7	28	84	11	102	25	14	32	27	1.94
3619477--3619673	107	1.8	107	81	6	247	31	12	26	28	1.93
3619610--3619724	51	2.3	51	83	10	146	33	10	25	31	1.89
3619425--3619873	237	1.9	237	85	3	618	32	13	25	27	1.93
3619904--3619969	28	2.3	29	74	7	73	28	15	25	30	1.96
3619977--3620099	51	2.4	51	77	0	147	39	9	20	30	1.85
3622469--3622523	20	2.8	20	100	0	110	45	14	14	25	1.83
3630107--3630693	79	7.4	79	84	1	719	28	25	12	33	1.93
3643049--3643115	26	2.7	24	82	11	80	85	5	5	2	0.84
3643049--3643115	23	3.0	21	82	6	62	85	5	5	2	0.84
3643088--3643127	7	5.6	7	90	3	62	82	0	15	2	0.77
3643049--3643115	24	2.9	23	82	10	66	85	5	5	2	0.84
3644119--3644838	61	11.9	61	85	5	888	26	27	18	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3644089--3644840	181	4.1	183	85	5	910	27	27	18	27	1.98
3644102--3644839	241	3.1	243	88	3	1082	27	26	18	26	1.98
3644821--3644921	41	2.4	42	86	3	141	24	24	13	36	1.92
3645620--3645671	13	4.2	13	85	9	81	28	13	17	40	1.87
3645621--3645666	24	1.9	24	100	0	92	28	13	19	39	1.89
3647559--3647603	22	2.0	22	91	8	74	31	8	26	33	1.87
3648012--3648619	79	7.7	78	84	2	678	27	24	14	34	1.94
3648012--3648605	157	3.8	158	86	1	744	27	24	14	33	1.94
3648012--3648605	236	2.5	237	84	2	730	27	24	14	33	1.94
3653167--3653202	14	2.5	15	86	13	58	47	33	0	19	1.50
3653790--3653837	22	2.2	21	82	10	53	16	16	12	54	1.72
3663315--3663383	33	2.1	33	83	5	86	37	17	11	33	1.86
3663431--3663457	13	2.1	13	100	0	54	40	14	14	29	1.86
3669926--3669968	21	2.0	21	81	0	50	30	11	4	53	1.57
3670086--3670124	15	2.6	15	79	0	51	28	10	5	56	1.54
3672223--3672282	19	3.0	20	78	7	77	40	18	10	31	1.84
3672263--3672289	13	2.1	13	100	0	54	40	14	14	29	1.86
3677278--3677339	20	3.0	20	80	11	81	38	11	19	30	1.87
3677280--3677363	42	2.0	42	88	2	125	40	11	16	30	1.85
3677280--3677355	21	3.7	21	75	8	75	42	11	14	31	1.82
3681049--3681074	13	2.0	13	100	0	52	38	15	15	30	1.88
3681031--3681094	33	2.0	32	87	3	92	39	18	14	28	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3682684--3682723	3	13.3	3	89	0	62	37	0	35	27	1.57
3685151--3685187	15	2.4	16	86	9	58	48	18	16	16	1.81
3687037--3687076	8	5.0	8	100	0	80	12	0	25	62	1.30
3687280--3687317	13	2.9	13	88	0	58	36	18	13	31	1.89
3689118--3689226	31	3.5	31	80	5	148	38	2	33	24	1.70
3689107--3689233	62	2.0	62	98	0	245	38	3	30	27	1.72
3689922--3689946	13	1.9	13	100	0	50	32	16	16	36	1.90
3689902--3689969	33	2.1	33	91	2	111	36	17	13	32	1.89
3689969--3690003	10	3.5	10	96	0	61	25	20	31	22	1.98
3704196--3704231	17	2.1	17	94	0	63	5	2	5	86	0.79

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