genome.fa.s25.2.7.7.80.10.50.1000.32.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   53   54   55   56   

This is table  32  of  56  ( 6609 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)
5414793--5414817	13	1.9	13	100	0	50	32	16	16	36	1.90
5414806--5414954	52	2.9	50	87	6	208	33	17	17	31	1.93
5419857--5419911	24	2.3	24	81	9	69	40	18	5	36	1.74
5420969--5421018	15	3.4	15	78	15	59	50	0	0	50	1.00
5421862--5422868	195	5.3	193	73	10	511	36	12	21	29	1.90
5421958--5422458	97	5.2	97	79	4	377	35	13	22	29	1.92
5422055--5422529	97	4.9	96	77	7	300	36	12	22	29	1.90
5424018--5424057	21	2.0	21	90	5	64	30	10	7	52	1.62
5424147--5424255	37	3.1	37	65	28	101	33	16	1	47	1.57
5424124--5424255	68	1.9	68	96	0	246	35	15	1	46	1.56
5435245--5435302	20	2.8	20	84	5	62	63	1	5	29	1.25
5436343--5436392	21	2.6	18	73	14	55	34	0	2	64	1.05
5438658--5438741	41	2.0	44	84	11	113	46	0	1	52	1.08
5440879--5440910	2	16.0	2	100	0	64	50	0	0	50	1.00
5447837--5447861	13	1.9	13	100	0	50	36	16	16	32	1.90
5447924--5447948	13	1.9	13	100	0	50	32	16	16	36	1.90
5451260--5451310	20	2.6	19	75	6	57	37	15	11	35	1.84
5451890--5452641	32	23.7	32	91	2	1135	18	18	33	29	1.95
5452624--5453663	27	38.0	27	91	2	1630	27	14	35	23	1.93
5452624--5453663	82	12.7	81	91	2	1630	27	14	35	23	1.93
5452624--5453663	109	9.5	109	91	2	1647	27	14	35	23	1.93
5454938--5454989	23	2.3	23	83	12	63	5	11	7	75	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5454970--5455012	15	2.8	16	79	13	54	4	18	11	65	1.42
5461135--5461183	23	2.1	23	100	0	98	67	8	8	16	1.40
5461135--5461189	23	2.5	22	94	5	94	61	9	10	18	1.54
5462103--5462177	20	3.8	20	76	3	71	41	12	12	34	1.79
5462100--5462177	40	2.0	39	84	2	102	41	12	11	34	1.80
5465784--5465918	70	1.9	70	86	0	189	44	17	8	29	1.79
5467276--5467322	17	2.7	18	86	3	60	23	10	10	55	1.65
5467293--5467387	29	3.3	29	81	0	118	21	8	10	60	1.56
5467293--5467419	58	2.2	58	87	2	175	19	7	11	60	1.55
5467314--5467416	29	3.6	29	76	7	102	20	6	12	60	1.55
5468860--5468884	13	1.9	13	100	0	50	40	8	20	32	1.81
5469523--5469551	13	2.1	14	93	6	51	31	0	0	68	0.89
5469819--5469875	30	1.9	30	82	7	71	40	1	0	57	1.09
5470110--5470141	2	16.0	2	100	0	64	50	0	0	50	1.00
5470705--5470748	3	14.7	3	100	0	88	0	34	0	65	0.93
5483098--5483137	20	2.0	21	90	5	64	70	2	0	27	1.01
5483101--5483142	14	3.2	13	83	9	50	71	2	0	26	0.98
5484120--5484154	7	4.9	7	92	3	52	54	0	0	45	0.99
5484173--5484227	8	7.3	7	91	8	58	47	0	1	50	1.11
5484179--5484228	2	25.5	2	95	4	93	50	0	0	50	1.00
5484376--5484400	2	12.5	2	100	0	50	52	0	0	48	1.00
5491680--5491709	6	5.2	6	92	8	53	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5492355--5492426	23	3.1	23	78	13	85	36	6	9	47	1.64
5492529--5492577	25	2.0	25	91	0	80	57	0	6	36	1.24
5492768--5492797	2	15.0	2	100	0	60	50	0	0	50	1.00
5496262--5496394	66	2.0	66	91	0	212	33	15	8	42	1.76
5496879--5496916	2	19.0	2	88	0	58	47	2	2	47	1.30
5500993--5501044	26	2.0	26	92	0	86	21	11	19	48	1.80
5502115--5502165	19	2.6	19	81	3	57	35	13	15	35	1.87
5503592--5503616	12	2.1	12	100	0	50	36	16	16	32	1.90
5503574--5503636	31	2.0	31	87	6	92	38	17	14	30	1.89
5505837--5505881	21	2.1	21	84	8	56	53	4	20	22	1.63
5507685--5507715	15	2.1	15	100	0	62	51	16	19	12	1.76
5509795--5509820	13	2.0	13	100	0	52	30	15	15	38	1.88
5512364--5512389	13	2.0	13	100	0	52	38	15	15	30	1.88
5512346--5512409	32	2.0	33	87	3	94	40	17	14	28	1.88
5519928--5519990	33	1.9	33	87	6	92	30	17	14	38	1.89
5523597--5523651	20	2.8	20	88	5	76	38	14	14	32	1.87
5524602--5525009	28	14.5	27	86	6	492	20	17	32	28	1.96
5526258--5526295	4	9.8	4	85	5	51	0	0	15	84	0.63
5526255--5526332	8	10.0	8	77	10	72	2	2	12	82	0.89
5526256--5526332	37	2.0	39	85	5	104	2	2	12	81	0.89
5526266--5526312	12	3.8	12	84	15	60	0	2	14	82	0.75
5542745--5542806	22	2.9	21	77	11	63	48	3	11	37	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5542881--5542952	20	3.7	20	79	3	74	33	16	16	33	1.92
5549681--5550061	79	4.8	79	77	7	360	35	10	24	29	1.89
5549681--5550061	159	2.4	159	81	3	430	35	10	24	29	1.89
5552863--5552906	2	22.0	2	100	0	88	50	0	0	50	1.00
5555483--5555511	14	2.1	14	100	0	58	34	13	37	13	1.85
5556866--5556916	16	3.6	16	68	29	51	43	0	1	54	1.11
5557822--5557875	22	2.5	20	77	14	54	46	5	7	40	1.55
5558654--5558699	19	2.4	19	88	0	65	36	0	0	63	0.95
5559729--5559772	23	1.9	23	85	0	61	52	2	2	43	1.26
5559883--5560061	85	2.1	85	92	1	297	45	12	13	28	1.80
5561148--5561194	24	2.0	23	84	8	60	34	2	0	63	1.06
5563222--5563284	29	2.2	28	77	11	65	47	0	0	52	1.00
5563244--5563283	15	2.7	15	82	17	57	42	0	0	57	0.98
5564201--5564231	2	15.5	2	100	0	62	51	0	0	48	1.00
5574111--5574135	6	4.2	6	100	0	50	32	20	0	48	1.50
5577340--5577401	26	2.3	26	86	5	79	50	4	1	43	1.33
5578198--5578232	4	8.8	4	100	0	70	25	0	25	48	1.51
5580073--5580120	18	2.6	18	83	6	51	41	4	0	54	1.20
5584479--5584514	18	2.0	18	88	0	54	50	0	2	47	1.15
5584519--5584568	22	2.3	22	96	0	91	40	0	2	58	1.10
5584565--5584675	21	5.3	22	70	18	69	45	0	2	51	1.15
5584830--5584888	16	3.7	16	80	8	66	35	1	5	57	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5588037--5588082	24	1.9	24	86	0	65	10	8	10	69	1.37
5590963--5591004	21	2.0	20	86	4	57	61	2	0	35	1.09
5592111--5592150	20	2.0	21	85	5	55	42	2	0	55	1.13
5592867--5592929	30	2.1	30	85	5	83	42	0	0	57	0.99
5592901--5592952	23	2.3	23	79	20	58	44	0	0	55	0.99
5609009--5609107	52	1.9	52	91	0	162	23	35	14	27	1.93
5612656--5612696	21	2.0	21	85	0	55	26	36	7	29	1.83
5614155--5614313	71	2.2	71	82	5	187	28	12	12	45	1.79
5614337--5614371	2	18.0	2	94	5	63	48	0	0	51	1.00
5614937--5615000	15	4.6	14	74	11	51	67	7	1	23	1.26
5615494--5615563	16	4.5	15	71	16	52	60	2	0	37	1.12
5615822--5615877	25	2.2	24	78	6	58	58	1	0	39	1.08
5616045--5616094	13	3.8	13	80	19	59	68	0	2	30	1.01
5618353--5618382	2	15.0	2	100	0	60	50	0	0	50	1.00
5618967--5619013	14	3.4	14	84	0	58	55	2	2	40	1.24
5626933--5626975	20	2.2	20	92	8	72	37	0	0	62	0.95
5628275--5628301	11	2.5	11	100	0	54	81	0	0	18	0.69
5628019--5628428	205	2.0	204	95	1	741	48	9	5	36	1.59
5628910--5628944	2	17.5	2	100	0	70	48	0	0	51	1.00
5629657--5629732	11	7.5	11	68	24	51	51	11	5	31	1.61
5629657--5629722	21	3.4	19	85	14	82	51	12	6	30	1.63
5629678--5629725	9	4.9	9	78	16	51	54	10	4	31	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5629657--5629732	21	3.8	21	80	15	81	51	11	5	31	1.61
5629665--5629763	21	4.9	21	78	8	75	51	12	5	31	1.60
5629861--5629919	11	5.6	11	69	18	54	49	11	1	37	1.50
5629860--5630038	21	8.6	21	78	10	156	49	8	4	36	1.54
5629950--5630055	31	3.5	31	74	5	90	52	4	2	39	1.37
5630261--5630318	20	3.0	20	73	12	57	56	3	6	32	1.42
5630258--5630338	10	8.1	10	69	14	51	55	3	4	35	1.39
5630325--5630370	21	2.2	21	92	0	74	52	10	4	32	1.56
5630344--5630397	27	2.0	27	88	0	81	55	12	3	27	1.54
5630325--5630418	48	2.0	48	89	0	143	55	9	4	30	1.51

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   53   54   55   56