genome.fa.s1.2.7.7.80.10.50.1000.21.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  21  of  52  ( 6211 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)
3256370--3256435	32	2.0	33	94	2	116	34	12	16	36	1.86
3256476--3256500	13	1.9	13	100	0	50	32	16	16	36	1.90
3256489--3256637	52	2.9	53	87	4	196	35	17	16	30	1.92
3267157--3267182	13	2.0	13	100	0	52	30	15	15	38	1.88
3267167--3267222	19	2.9	19	84	5	76	32	16	12	39	1.85
3267168--3267221	20	2.8	19	88	2	72	33	14	11	40	1.82
3269079--3269132	24	2.2	24	96	0	99	57	7	20	14	1.61
3277264--3277317	21	2.7	19	85	5	72	37	12	16	33	1.87
3277264--3277380	19	6.7	19	72	23	87	36	12	17	32	1.88
3277286--3277388	32	3.2	32	90	0	170	34	12	19	33	1.89
3279693--3279718	12	2.2	12	100	0	52	42	15	15	26	1.87
3283252--3283302	20	2.5	20	96	0	93	23	23	19	33	1.97
3289474--3289513	20	2.0	21	90	5	64	77	2	2	17	0.99
3289582--3289642	31	2.0	29	90	6	95	36	18	26	19	1.94
3290393--3290607	110	2.0	110	94	1	378	23	7	18	51	1.71
3298848--3298920	20	3.6	20	81	3	101	31	19	13	35	1.91
3298827--3298920	41	2.3	41	96	0	170	30	18	12	38	1.88
3298827--3298902	21	3.7	21	78	3	91	30	17	11	40	1.85
3301867--3301913	21	2.3	21	82	13	62	42	14	17	25	1.87
3302783--3302853	35	2.0	35	94	0	124	33	14	15	36	1.87
3302881--3302905	13	1.9	13	100	0	50	36	16	16	32	1.90
3302968--3302992	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3303560--3303672	52	2.2	52	85	0	145	36	18	22	23	1.95
3303770--3304066	32	9.2	32	87	4	402	20	17	33	28	1.95
3303774--3304067	65	4.5	66	90	2	418	20	17	33	28	1.95
3303770--3304062	97	3.0	97	93	1	471	19	17	33	29	1.95
3304074--3304254	71	2.6	68	84	6	247	32	12	34	20	1.90
3304053--3304276	105	2.2	102	85	5	290	31	11	35	21	1.89
3304053--3304392	34	10.3	35	74	12	256	30	12	34	22	1.90
3304213--3304391	61	2.9	61	90	2	261	29	12	35	22	1.91
3304372--3304615	30	7.9	29	75	14	186	28	17	30	23	1.97
3304389--3304616	95	2.4	94	82	6	268	29	17	29	23	1.97
3304384--3304611	61	3.7	61	78	10	212	28	17	30	23	1.97
3304403--3304616	31	6.9	30	73	12	164	29	16	30	23	1.96
3304715--3304752	16	2.3	17	86	4	51	26	5	23	44	1.74
3311955--3312025	35	2.0	35	94	0	124	33	14	15	36	1.87
3312140--3312164	13	1.9	13	100	0	50	32	16	16	36	1.90
3312732--3312844	52	2.2	52	88	0	163	36	18	22	23	1.95
3312798--3312879	43	1.9	43	92	0	137	28	19	29	23	1.98
3312942--3313238	32	9.2	32	87	4	393	19	17	33	29	1.95
3312946--3313239	65	4.5	66	89	2	409	19	17	33	29	1.95
3312942--3313234	97	3.0	97	92	1	462	18	17	33	30	1.94
3313246--3313426	71	2.6	68	82	6	229	33	12	33	20	1.90
3313225--3313448	105	2.2	102	83	5	272	32	11	34	21	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3313225--3313564	34	10.3	35	73	12	238	31	12	34	22	1.91
3313385--3313563	61	2.9	61	90	2	261	29	12	35	22	1.91
3313544--3313787	30	7.9	29	75	14	186	28	17	30	23	1.97
3313561--3313788	95	2.4	94	82	6	268	29	17	29	23	1.97
3313556--3313783	61	3.7	61	78	10	212	28	17	30	23	1.97
3313575--3313788	31	6.9	30	73	12	164	29	16	30	23	1.96
3313887--3313924	16	2.3	17	86	4	51	26	5	23	44	1.74
3321187--3321311	52	2.4	52	89	0	187	30	18	16	35	1.92
3321187--3321336	52	2.9	51	84	4	185	32	18	16	34	1.92
3321376--3321442	33	2.0	33	85	0	89	40	16	11	31	1.85
3321398--3321422	13	1.9	13	100	0	50	32	16	16	36	1.90
3326678--3326846	43	4.0	43	84	3	209	14	31	16	37	1.89
3326678--3326846	85	2.0	85	90	0	266	14	31	16	37	1.89
3327445--3327515	31	2.3	31	82	7	90	42	21	21	15	1.89
3328245--3328443	98	2.0	98	98	0	380	24	6	18	50	1.71
3329118--3329398	151	1.9	151	81	3	341	29	16	15	39	1.89
3331822--3331895	20	3.7	19	83	7	94	28	16	12	43	1.83
3334295--3334370	28	2.7	28	83	4	91	21	31	21	26	1.98
3334248--3334560	110	2.9	107	75	12	316	26	26	15	32	1.95
3334433--3334763	78	4.2	78	80	6	348	26	25	14	33	1.94
3342851--3343479	315	2.0	314	98	0	1222	20	9	28	40	1.84
3343919--3343973	20	2.8	20	80	0	65	45	14	14	25	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3348004--3348044	21	2.0	21	85	9	57	39	12	9	39	1.76
3348084--3348154	20	3.6	19	77	7	70	40	16	12	29	1.86
3348124--3348261	54	2.6	54	97	1	260	37	18	17	26	1.93
3348171--3348208	20	1.9	20	94	0	67	42	18	10	28	1.83
3348295--3348352	23	2.5	23	82	2	71	29	25	6	37	1.82
3348406--3348431	13	2.0	13	100	0	52	30	15	23	30	1.95
3352154--3352178	13	1.9	13	100	0	50	44	16	8	32	1.76
3353849--3353889	21	2.0	21	85	9	57	39	12	9	39	1.76
3353929--3353999	20	3.6	19	77	7	70	40	16	12	29	1.86
3354141--3354166	13	2.0	13	100	0	52	30	15	23	30	1.95
3357280--3357305	13	2.0	13	100	0	52	30	15	15	38	1.88
3359161--3359186	13	2.0	13	100	0	52	30	15	15	38	1.88
3359893--3359936	21	2.1	21	83	8	54	25	31	4	38	1.76
3361743--3361768	13	2.0	13	100	0	52	38	15	15	30	1.88
3365690--3365734	21	2.1	21	84	8	56	22	20	4	53	1.63
3375992--3376044	20	2.6	21	85	8	74	28	13	16	41	1.86
3375992--3376050	20	3.0	19	85	7	73	25	11	20	42	1.86
3382473--3382823	175	2.0	175	98	0	675	36	18	23	20	1.95
3391696--3391793	19	5.9	17	72	27	86	32	13	16	37	1.87
3391699--3391801	32	3.2	32	94	0	179	32	13	17	36	1.89
3391717--3391775	13	4.1	13	73	23	55	32	15	15	37	1.88
3391846--3391870	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3391898--3392006	51	2.1	52	91	1	175	38	17	14	29	1.89
3392851--3392891	21	1.9	22	90	5	66	21	17	17	43	1.87
3397595--3397635	11	3.5	11	81	12	55	2	19	0	78	0.87
3397595--3397649	24	2.3	22	77	17	56	9	20	0	70	1.13
3397990--3398034	22	2.0	22	82	4	54	17	17	15	48	1.81
3398734--3398839	45	2.2	48	81	6	128	29	21	30	18	1.97
3398872--3400317	32	46.8	32	89	3	1972	18	18	32	30	1.95
3398884--3400317	462	3.1	462	94	2	2427	17	18	32	30	1.95
3398884--3400308	399	3.5	402	93	2	2254	17	19	32	30	1.95
3400300--3401557	27	46.0	27	93	2	2120	27	15	35	21	1.93
3400300--3401557	82	15.3	81	94	1	2120	27	15	35	21	1.93
3400303--3401557	438	2.9	437	96	0	2282	27	15	35	21	1.93
3401521--3401609	46	1.9	46	97	0	169	38	11	26	23	1.89
3401577--3401634	30	1.9	31	89	3	91	32	15	27	24	1.95
3409428--3409468	11	3.5	11	81	12	55	2	19	0	78	0.87
3409428--3409482	24	2.3	22	77	17	56	9	20	0	70	1.13
3412439--3412474	18	2.0	18	94	0	63	25	27	19	27	1.99
3412810--3412859	27	1.9	26	84	8	66	44	2	24	30	1.65
3412871--3412912	21	2.0	21	85	0	57	38	2	28	30	1.70
3413537--3413563	13	2.1	13	100	0	54	29	14	14	40	1.86
3416610--3416694	37	2.3	36	76	8	89	21	25	10	42	1.85
3416532--3416816	121	2.4	119	84	2	349	21	26	11	40	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3416628--3416945	155	2.1	152	80	5	345	22	24	12	39	1.90
3416848--3416967	36	3.4	36	74	10	95	20	27	11	40	1.87
3417045--3417624	148	3.9	148	88	1	795	30	24	24	20	1.98
3417472--3417544	31	2.4	30	81	4	74	30	30	20	19	1.97
3417004--3417661	297	2.2	297	84	3	837	31	25	23	19	1.98
3417663--3417732	31	2.3	31	87	0	95	32	30	25	11	1.91
3417682--3417750	31	2.2	31	89	0	102	26	27	31	14	1.95
3422966--3423043	20	3.9	20	79	3	95	46	10	10	33	1.72
3428186--3428621	164	2.7	165	84	4	546	38	12	12	36	1.81
3429942--3430366	167	2.6	165	84	4	516	51	7	10	30	1.63

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