genome.fa.s1.2.7.7.80.10.50.1000.26.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  26  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)
4289334--4289517	86	2.2	84	80	8	194	36	17	13	32	1.89
4289453--4289581	52	2.5	52	93	0	231	35	17	17	28	1.93
4294052--4294107	19	2.9	19	83	2	67	32	14	16	37	1.88
4300893--4300972	31	2.6	31	81	0	97	46	10	16	27	1.78
4301725--4302089	48	7.6	48	84	3	407	35	15	26	21	1.94
4301768--4302029	142	1.8	142	92	0	443	35	14	28	21	1.93
4302062--4302383	95	3.4	94	81	5	380	31	15	25	26	1.96
4302164--4302338	52	3.5	52	71	13	170	34	17	23	24	1.96
4302212--4302412	43	4.5	43	79	10	222	31	16	26	25	1.96
4302316--4302384	22	3.2	22	62	25	56	30	14	30	24	1.95
4302432--4302633	30	6.5	32	82	6	236	16	18	35	29	1.93
4302432--4302633	62	3.2	62	88	2	289	16	18	35	29	1.93
4302445--4302897	28	15.5	28	79	7	361	21	17	30	30	1.96
4304144--4304211	17	3.9	17	76	16	68	0	2	16	80	0.82
4304144--4304211	8	8.0	8	77	18	66	0	2	16	80	0.82
4304146--4304210	9	6.8	9	83	11	76	0	3	15	81	0.81
4317088--4317223	71	1.9	71	88	5	204	43	13	16	27	1.84
4317138--4317234	51	1.9	51	91	4	160	43	14	15	26	1.85
4322594--4323010	28	14.2	28	78	9	336	28	30	17	22	1.97
4322596--4322991	58	6.8	57	78	8	223	28	31	17	22	1.97
4322601--4322896	86	3.5	84	82	7	321	29	30	17	22	1.96
4322594--4323009	115	3.6	113	78	9	374	28	31	18	22	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4322651--4322991	143	2.3	146	82	8	390	28	31	17	22	1.97
4322596--4323019	63	7.2	61	79	9	263	28	31	17	22	1.97
4324748--4324820	20	3.6	20	81	3	101	35	13	19	31	1.91
4324766--4324841	21	3.7	21	80	3	100	42	11	17	28	1.84
4324748--4324841	41	2.3	41	98	0	179	39	12	18	29	1.88
4324880--4324905	13	2.0	13	100	0	52	38	15	15	30	1.88
4328967--4328997	15	2.1	15	93	0	53	48	16	22	12	1.80
4331012--4331089	20	3.6	21	73	15	70	25	12	16	44	1.83
4331076--4331114	13	3.0	13	96	0	69	30	17	15	35	1.91
4333598--4333670	20	3.6	20	81	3	101	35	13	19	31	1.91
4333616--4333691	21	3.7	21	78	3	91	40	11	17	30	1.85
4333598--4333691	41	2.3	41	96	0	170	38	12	18	30	1.88
4333730--4333755	13	2.0	13	100	0	52	38	15	15	30	1.88
4336080--4336122	21	2.0	21	82	8	52	4	27	4	62	1.35
4337265--4337320	30	1.9	30	85	7	80	58	19	8	12	1.60
4343139--4343201	32	1.9	33	83	3	83	31	14	12	41	1.83
4344781--4344805	12	2.1	12	100	0	50	32	16	16	36	1.90
4344761--4344823	31	2.0	31	87	6	92	30	15	15	38	1.89
4344865--4344937	20	3.6	20	81	3	101	31	19	13	35	1.91
4344844--4344937	41	2.3	41	96	0	170	30	18	12	38	1.88
4344844--4344919	21	3.7	21	78	3	91	30	17	11	40	1.85
4349780--4350159	154	2.5	153	84	5	480	38	19	17	25	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4352517--4352591	28	2.7	29	81	12	93	24	18	32	25	1.97
4352577--4352756	52	3.4	52	76	4	157	33	10	23	32	1.88
4355116--4355141	13	2.0	13	100	0	52	38	15	15	30	1.88
4355095--4355161	33	2.0	33	88	0	98	43	16	14	25	1.86
4355181--4355248	19	3.9	18	73	23	74	39	14	11	33	1.83
4355184--4355246	32	2.0	32	93	0	108	38	15	12	33	1.86
4355522--4355574	19	2.7	19	76	2	61	33	18	13	33	1.90
4355624--4355686	13	5.3	13	69	21	57	31	19	14	34	1.91
4355607--4355687	33	2.5	33	95	0	144	29	18	17	34	1.94
4355607--4355669	20	3.5	20	68	28	68	30	17	17	34	1.93
4355607--4355708	33	3.1	33	88	5	136	30	17	17	34	1.93
4355731--4355768	20	2.0	20	94	5	69	36	10	15	36	1.82
4359282--4359355	20	3.7	20	82	8	78	29	17	13	39	1.88
4361779--4361816	13	2.9	13	96	0	67	31	15	18	34	1.92
4363897--4363927	15	2.1	15	93	0	53	12	22	16	48	1.80
4367993--4368018	13	2.0	13	100	0	52	30	15	15	38	1.88
4367973--4368036	32	2.0	33	93	3	112	28	12	15	43	1.83
4367973--4368036	19	3.6	19	72	25	68	28	12	15	43	1.83
4368067--4368140	20	3.7	20	82	8	78	29	17	13	39	1.88
4369187--4369261	20	3.8	20	85	0	105	32	13	13	41	1.83
4369247--4369312	31	2.1	31	91	0	105	21	19	15	43	1.87
4369247--4369320	31	2.4	31	88	0	94	22	18	16	41	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4381242--4381296	20	2.8	20	88	5	76	32	14	12	40	1.84
4386443--4386486	21	2.0	22	86	4	63	31	4	20	43	1.72
4387150--4387179	13	2.3	13	94	0	51	36	16	10	36	1.82
4387133--4387202	33	2.1	33	84	10	90	32	12	17	37	1.87
4388995--4389563	166	3.4	166	82	6	618	49	10	9	30	1.70
4389074--4389661	166	3.5	165	81	7	452	50	9	9	30	1.66
4388972--4389661	332	2.1	330	79	8	720	49	9	10	30	1.68
4390781--4391082	84	3.6	84	78	4	306	36	14	31	18	1.91
4390949--4391071	42	2.9	42	68	9	106	32	14	33	19	1.92
4391167--4391764	44	13.6	43	71	11	322	40	16	21	21	1.91
4391167--4391673	132	3.8	132	85	2	624	40	16	21	21	1.91
4391777--4392105	48	6.8	48	78	6	288	44	20	15	19	1.86
4391829--4392105	147	1.9	148	87	3	416	44	21	15	19	1.87
4392100--4392223	35	3.5	34	72	4	95	41	12	24	21	1.88
4393006--4393040	17	2.1	16	89	5	52	5	14	0	80	0.89
4392996--4393032	19	2.0	19	89	5	58	5	10	0	83	0.79
4393356--4393407	12	4.4	11	77	15	50	7	7	1	82	0.91
4394740--4394978	104	2.3	106	83	2	286	45	9	23	21	1.81
4395001--4395063	33	2.0	32	81	12	76	46	17	22	14	1.84
4395096--4395301	67	3.1	66	79	4	216	47	16	20	15	1.83
4395253--4395317	34	1.9	34	90	0	103	50	21	16	10	1.75
4395253--4395334	34	2.4	34	85	0	101	51	20	18	9	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4395338--4395572	67	3.5	66	75	11	235	46	14	20	18	1.83
4395575--4395919	133	2.6	134	78	2	327	49	16	17	16	1.80
4395576--4395919	67	5.2	66	77	5	253	49	16	17	16	1.80
4399178--4399219	22	2.0	21	86	13	59	2	7	4	85	0.80
4399572--4399973	147	2.7	146	77	14	392	52	7	5	33	1.54
4401113--4401253	42	3.4	42	75	14	121	52	14	17	16	1.75
4401067--4401253	84	2.2	85	82	6	220	50	14	18	16	1.79
4401296--4401672	44	8.8	43	74	12	240	40	16	22	19	1.91
4401296--4401530	87	2.7	88	81	4	269	41	16	22	19	1.90
4401543--4401609	34	2.0	34	82	5	82	35	20	20	22	1.96
4401499--4401652	78	2.0	78	84	5	204	38	18	22	20	1.93
4401728--4401826	35	2.8	35	81	1	117	43	15	20	21	1.88
4402123--4402245	45	2.7	46	85	2	167	41	14	22	21	1.89
4401772--4402202	81	5.3	81	77	4	364	43	14	20	20	1.87
4402063--4402329	128	2.1	125	82	4	313	43	15	20	20	1.87
4403265--4403317	21	2.5	21	79	11	63	7	16	1	73	1.15
4403279--4403345	31	2.2	31	83	0	80	1	14	5	77	1.03
4403289--4403364	31	2.5	30	85	8	93	1	10	9	78	1.01
4403289--4403390	16	5.9	17	65	17	50	2	8	9	78	1.06
4403311--4403375	20	3.2	20	77	18	64	1	6	13	78	1.01
4403310--4403356	10	4.7	10	79	10	51	0	6	10	82	0.82
4403311--4403375	21	3.2	21	73	18	57	1	6	13	78	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4403699--4403724	9	2.9	9	100	0	52	11	19	0	69	1.18
4403723--4403753	14	2.2	14	94	0	53	0	16	0	83	0.64
4405980--4406024	15	2.9	15	81	12	56	31	24	8	35	1.86
4412605--4412720	52	2.2	52	90	0	178	41	13	14	30	1.85
4412750--4412823	21	3.6	20	83	7	78	29	18	13	37	1.90
4414827--4414853	13	2.1	13	100	0	54	29	14	14	40	1.86
4414807--4414868	32	1.9	33	90	3	99	27	12	14	45	1.82
4417397--4417432	13	2.8	13	95	0	63	30	13	19	36	1.91
4419506--4419536	15	2.1	15	93	0	53	12	22	16	48	1.80
4423614--4423640	13	2.1	13	100	0	54	29	14	14	40	1.86

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