genome.fa.s25.2.7.7.80.10.50.1000.33.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  33  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)
5630372--5630456	21	4.0	21	74	6	73	51	4	5	37	1.47
5630475--5630606	20	6.4	21	72	12	96	51	9	5	33	1.58
5630526--5630606	22	3.8	22	75	14	89	53	9	4	32	1.56
5630567--5630639	12	6.6	12	65	16	50	56	10	4	28	1.52
5630522--5630736	21	10.9	19	66	20	79	52	9	5	32	1.57
5630668--5630746	41	1.9	41	81	0	95	55	7	5	31	1.50
5630785--5630876	45	2.0	46	87	2	132	55	3	8	32	1.47
5630573--5631053	21	22.5	21	68	15	116	51	8	8	31	1.62
5630786--5630948	67	2.4	66	82	2	191	50	6	10	31	1.62
5630985--5631073	21	4.3	21	84	5	74	53	6	5	33	1.50
5633949--5633986	20	1.9	20	84	10	51	34	0	7	57	1.28
5633949--5633988	21	2.0	20	85	5	53	35	0	7	57	1.27
5634665--5634701	2	18.5	2	100	0	74	51	0	0	48	1.00
5634701--5634736	2	18.0	2	100	0	72	50	0	50	0	1.00
5635537--5635593	26	2.1	28	81	15	68	31	1	0	66	1.02
5636556--5636822	133	2.0	134	84	5	353	43	9	2	44	1.51
5637109--5637138	2	15.0	2	100	0	60	50	0	0	50	1.00
5637321--5637363	3	14.7	3	90	4	70	32	0	2	65	1.06
5638045--5638115	22	3.2	21	78	11	61	64	2	1	30	1.16
5641579--5641603	13	1.9	13	100	0	50	16	8	12	64	1.49
5645150--5645174	1	25.0	1	100	0	50	0	0	0	100	0.00
5646136--5646180	16	2.8	16	82	0	63	35	0	15	48	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5646174--5646201	2	14.0	2	100	0	56	0	0	50	50	1.00
5648450--5648501	20	2.6	19	85	8	68	55	0	1	42	1.10
5648609--5648654	19	2.2	21	85	11	60	30	4	0	65	1.12
5648604--5648654	22	2.3	23	86	3	68	31	3	0	64	1.11
5651013--5651045	16	2.1	16	88	11	50	36	18	6	39	1.75
5652545--5652583	20	2.0	20	84	0	51	46	0	0	53	1.00
5652999--5653070	23	3.0	24	80	11	69	65	0	0	34	0.93
5653097--5653130	16	2.1	17	88	5	52	64	0	0	35	0.94
5654106--5654168	28	2.2	29	80	5	85	53	0	0	46	1.00
5654686--5654714	12	2.3	13	94	5	51	75	6	3	13	1.13
5654916--5654949	2	17.0	2	100	0	68	50	0	0	50	1.00
5659556--5659669	57	2.0	57	100	0	228	28	8	24	38	1.85
5663681--5663711	2	15.5	2	100	0	62	51	0	0	48	1.00
5672916--5672987	32	2.2	33	95	2	128	34	11	19	34	1.87
5676915--5676975	32	1.9	32	89	0	95	42	26	14	16	1.87
5678657--5678693	3	12.3	3	100	0	74	35	0	0	64	0.94
5679451--5679493	18	2.4	18	84	7	52	46	2	4	46	1.36
5681309--5681357	26	1.9	25	84	12	64	30	8	2	59	1.38
5682315--5682348	14	2.5	13	90	4	50	41	2	0	55	1.15
5683456--5683557	41	2.4	42	77	9	109	34	9	8	47	1.68
5684656--5684686	2	15.5	2	100	0	62	48	0	0	51	1.00
5685531--5685606	34	2.2	36	81	9	86	46	5	5	43	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5686221--5686250	15	2.0	15	93	0	51	40	3	0	56	1.16
5693354--5693389	18	2.0	18	89	10	56	27	2	2	66	1.19
5693665--5693695	3	10.3	3	100	0	62	67	0	0	32	0.91
5698641--5698674	2	17.0	2	93	0	59	50	47	0	2	1.16
5703171--5703199	2	15.0	2	92	7	51	48	0	0	51	1.00
5704238--5704276	17	2.3	17	86	0	51	64	7	5	23	1.40
5704327--5704417	40	2.3	39	81	12	105	65	2	4	27	1.23
5704345--5704397	26	2.1	26	82	10	65	66	1	5	26	1.25
5704461--5704585	40	3.1	39	73	6	117	45	13	20	20	1.84
5705391--5705665	120	2.3	120	80	8	319	46	17	13	21	1.83
5705300--5705665	60	6.1	60	76	7	278	45	16	16	21	1.86
5706505--5706721	108	2.0	109	83	2	276	41	10	13	34	1.79
5707535--5707560	2	13.0	2	100	0	52	50	0	0	50	1.00
5712319--5712360	20	2.1	20	86	0	57	9	7	0	83	0.81
5712309--5712357	23	2.1	23	81	7	55	8	8	2	81	0.94
5712517--5712553	18	2.0	19	94	5	67	64	0	5	29	1.15
5719655--5719696	2	21.0	2	90	0	66	45	0	4	50	1.23
5721290--5721334	23	1.9	24	86	4	65	57	0	4	37	1.19
5724279--5724340	16	4.1	16	77	10	76	59	1	0	38	1.07
5728345--5728382	19	2.1	18	85	14	51	47	10	26	15	1.78
5733836--5733887	27	1.9	27	84	0	68	38	13	23	25	1.91
5736321--5736434	51	2.2	51	93	0	192	37	20	7	35	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5738537--5738565	15	2.0	15	93	6	51	82	0	10	6	0.83
5743180--5743222	2	21.5	2	95	0	77	48	2	0	48	1.14
5744284--5744326	22	1.9	23	85	4	61	32	0	0	67	0.91
5744995--5745043	21	2.3	22	75	10	57	67	0	2	30	1.02
5746163--5746206	18	2.3	20	75	25	51	36	0	4	59	1.18
5746606--5746648	22	2.0	22	81	9	52	37	0	4	58	1.19
5747083--5747141	27	2.2	27	80	14	68	66	3	5	25	1.28
5747156--5747195	19	2.1	19	86	9	55	67	2	7	22	1.28
5749711--5749906	98	2.0	98	97	0	374	28	17	18	35	1.94
5750409--5750929	79	6.6	80	75	7	436	28	25	12	33	1.93
5750409--5750929	158	3.3	157	82	4	591	28	25	12	33	1.93
5750410--5750899	236	2.1	237	80	5	544	27	24	13	34	1.93
5750409--5750914	157	3.2	155	84	3	528	27	25	12	34	1.92
5761250--5761274	13	1.9	13	100	0	50	36	16	16	32	1.90
5763317--5763368	19	2.7	20	87	6	79	42	15	13	28	1.85
5764131--5764807	62	11.0	62	82	4	701	25	23	18	31	1.97
5764131--5764806	125	5.5	124	83	5	807	25	23	18	31	1.97
5764816--5765657	44	19.8	44	70	18	425	20	25	12	42	1.86
5764817--5765713	167	5.3	168	83	6	963	19	25	12	42	1.86
5765023--5765051	9	3.2	9	100	0	58	10	31	0	58	1.31
5769795--5769866	27	2.7	27	82	0	81	29	34	9	26	1.88
5769823--5770029	97	2.1	96	83	2	272	28	22	10	39	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5769823--5770066	97	2.5	95	79	7	258	27	22	11	37	1.89
5771013--5771038	13	2.0	13	100	0	52	30	15	15	38	1.88
5770993--5771056	33	2.0	33	90	3	103	26	14	17	42	1.87
5772707--5772778	19	3.7	19	75	16	67	52	0	0	47	1.00
5772707--5772760	20	2.8	20	86	8	67	50	0	0	50	1.00
5772746--5772787	14	3.0	14	83	10	50	59	0	0	40	0.97
5773864--5773921	27	2.1	27	81	6	64	43	0	5	51	1.24
5784153--5784227	39	1.9	39	86	7	109	44	2	0	53	1.14
5784548--5784581	2	17.0	2	100	0	68	50	0	0	50	1.00
5786691--5786755	32	2.0	32	96	0	121	33	0	23	43	1.54
5788661--5788703	14	3.0	14	80	6	50	41	0	0	58	0.98
5788694--5788741	22	2.1	24	84	7	64	33	2	0	64	1.05
5792588--5792615	3	9.3	3	100	0	56	32	0	0	67	0.91
5793211--5793279	32	2.2	31	89	7	104	56	1	0	42	1.08
5793205--5793267	18	3.6	19	70	27	59	55	1	0	42	1.09
5793257--5793300	19	2.3	19	88	0	61	63	2	0	34	1.07
5793752--5793788	19	1.9	19	89	10	58	62	0	0	37	0.96
5794984--5795040	29	1.9	30	86	10	82	36	0	3	59	1.14
5794973--5795047	30	2.5	31	77	12	86	38	0	2	58	1.12
5795014--5795071	18	3.4	18	72	9	50	37	0	0	62	0.96
5796066--5796136	5	14.4	5	69	19	51	61	0	1	36	1.05
5796089--5796138	11	4.5	11	83	11	59	66	0	0	34	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5796429--5796478	5	9.8	5	89	10	75	36	0	0	64	0.94
5796425--5796476	16	3.3	16	97	2	97	36	0	0	63	0.95
5796433--5796488	21	2.7	21	89	8	80	35	0	0	64	0.94
5796428--5796510	11	8.0	10	80	12	64	31	1	1	66	1.07
5798161--5798204	19	2.2	20	84	4	54	63	0	2	34	1.07
5799391--5799427	2	18.5	2	100	0	74	51	0	0	48	1.00
5799608--5799642	2	17.5	2	100	0	70	48	0	0	51	1.00
5802592--5802631	14	2.6	15	84	15	55	47	22	5	25	1.71
5802599--5802626	14	2.0	14	100	0	56	50	21	7	21	1.72
5808096--5808177	44	1.9	44	80	14	100	58	0	0	41	0.98

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