genome.fa.s8.2.7.7.80.10.50.1000.25.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   

This is table  25  of  33  ( 3942 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)
4303283--4303331	22	2.4	22	83	16	61	51	0	0	48	1.00
4305158--4305188	16	1.9	16	93	0	53	41	0	0	58	0.98
4306328--4306365	15	2.4	16	82	13	51	39	0	0	60	0.97
4313891--4313931	19	2.0	22	86	13	61	4	17	0	78	0.93
4324511--4324563	2	26.5	2	100	0	106	49	0	50	0	1.00
4327220--4327263	3	14.7	3	100	0	88	0	34	0	65	0.93
4327948--4328004	30	1.9	29	85	3	78	40	0	5	54	1.23
4329178--4329251	29	2.6	28	78	6	69	58	0	1	40	1.07
4329213--4329270	19	3.1	19	72	22	59	55	0	0	44	0.99
4329204--4329282	38	2.2	37	82	15	94	54	0	1	44	1.08
4329311--4329352	22	1.9	21	85	9	57	33	0	7	59	1.25
4330227--4330280	21	2.4	24	79	11	62	37	0	0	62	0.95
4331065--4331098	17	1.9	18	88	5	52	61	8	2	26	1.40
4340576--4340606	14	2.1	15	94	5	55	54	0	0	45	0.99
4342962--4342995	4	8.5	4	100	0	68	26	0	23	50	1.50
4343412--4343479	23	2.9	23	78	8	66	42	2	0	54	1.15
4343440--4343480	16	2.5	17	80	11	59	39	0	0	60	0.96
4344993--4345033	2	21.0	2	95	5	75	48	0	0	51	1.00
4347199--4347242	23	2.0	23	90	4	72	40	4	25	29	1.75
4351628--4351666	20	2.0	20	89	0	60	15	5	2	76	1.06
4352903--4352990	32	2.7	31	87	6	122	42	2	5	50	1.38
4354131--4354203	11	7.0	11	73	14	57	63	4	1	31	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4354478--4354521	18	2.4	18	85	7	54	59	4	9	27	1.48
4354913--4354963	17	3.1	17	75	8	52	72	3	1	21	1.11
4356960--4357042	42	2.0	42	100	0	166	19	16	25	38	1.92
4357165--4357423	132	2.0	132	94	0	455	24	22	23	29	1.99
4360723--4360790	16	4.1	17	74	16	54	54	1	0	44	1.09
4360713--4360791	32	2.5	31	84	12	90	53	1	1	44	1.16
4360722--4360792	17	4.5	15	75	14	63	56	1	0	42	1.08
4368648--4368688	20	2.1	20	90	4	66	53	0	0	46	1.00
4370139--4370204	33	2.0	33	96	0	123	19	10	30	39	1.86
4370217--4370278	22	2.8	22	74	13	65	66	0	0	33	0.92
4370242--4370281	5	8.0	5	83	10	55	60	0	0	40	0.97
4370230--4370299	17	4.1	17	74	15	54	61	0	4	34	1.16
4370223--4370281	15	4.3	14	83	12	61	64	0	0	35	0.94
4373188--4373217	2	15.0	2	100	0	60	50	0	0	50	1.00
4373578--4373620	21	2.0	22	86	8	63	48	2	11	37	1.52
4374293--4374354	16	3.7	18	73	14	53	59	0	1	38	1.07
4374280--4374372	29	3.1	31	78	19	83	58	0	1	40	1.05
4374299--4374372	33	2.4	29	82	15	78	56	0	1	41	1.07
4374477--4374510	3	11.3	3	100	0	68	35	0	0	64	0.94
4375505--4375587	22	3.7	22	77	16	66	59	0	1	39	1.05
4375545--4375597	16	3.5	14	72	18	52	54	0	0	45	0.99
4375551--4375602	16	3.2	16	72	22	54	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4375505--4375575	14	5.8	12	74	21	58	60	0	1	38	1.06
4377440--4377556	50	2.4	49	78	8	114	33	10	14	41	1.80
4382972--4383000	2	14.5	2	100	0	58	0	51	0	48	1.00
4383986--4384027	18	2.3	18	87	0	57	38	40	16	4	1.70
4385156--4385423	129	2.1	129	93	2	461	37	8	15	38	1.79
4387011--4387043	17	1.9	17	100	0	66	36	9	6	48	1.60
4397440--4397465	2	13.0	2	100	0	52	50	0	0	50	1.00
4398479--4398519	3	13.7	3	100	0	82	31	0	0	68	0.90
4400055--4400095	19	2.2	18	86	4	55	41	0	2	56	1.13
4400037--4400112	26	2.9	25	73	21	66	42	0	2	55	1.14
4401562--4401615	28	1.9	28	88	0	81	25	3	22	48	1.67
4402632--4402658	2	13.5	2	100	0	54	51	0	0	48	1.00
4403232--4403264	12	2.8	12	90	4	50	0	12	0	87	0.53
4406479--4406523	2	22.5	2	95	0	81	0	46	0	53	1.00
4406540--4406570	2	15.5	2	93	0	53	54	0	45	0	0.99
4410590--4410620	3	10.3	3	100	0	62	0	35	0	64	0.94
4413570--4413662	48	1.9	48	84	0	123	37	12	29	20	1.90
4420018--4420069	16	3.2	16	71	13	52	46	0	0	53	1.00
4420177--4420201	2	12.5	2	100	0	50	52	0	0	48	1.00
4421899--4421927	2	14.5	2	100	0	58	48	0	0	51	1.00
4426337--4426378	19	2.2	20	86	4	59	59	0	2	38	1.10
4430545--4430609	13	4.8	13	72	12	51	33	0	1	64	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4433859--4433895	18	2.0	19	89	5	58	62	0	0	37	0.96
4433953--4433986	18	1.9	17	88	5	50	20	14	0	64	1.28
4434729--4434769	3	13.7	3	100	0	82	0	34	0	65	0.93
4435210--4435240	2	15.5	2	100	0	62	51	0	0	48	1.00
4437690--4437750	22	2.7	22	72	23	54	37	1	0	60	1.07
4438082--4438145	20	3.1	20	86	4	74	56	0	1	42	1.09
4438091--4438162	20	3.6	20	73	17	60	55	0	1	43	1.08
4438122--4438171	24	2.2	23	86	10	68	60	0	2	38	1.09
4444014--4444039	1	26.0	1	100	0	52	100	0	0	0	0.00
4448311--4448352	22	1.9	22	85	9	59	50	2	0	47	1.14
4449746--4449784	17	2.2	18	90	4	62	43	10	0	46	1.37
4450064--4450172	10	10.9	10	69	20	59	60	0	0	39	0.97
4450061--4450141	27	3.3	23	75	20	60	66	0	0	33	0.92
4450063--4450141	25	3.1	27	75	20	73	65	0	0	34	0.93
4450071--4450141	23	2.9	23	76	21	63	63	0	0	36	0.95
4450137--4450198	26	2.3	28	78	18	69	51	0	0	48	1.00
4450584--4450619	17	2.1	17	89	0	54	41	0	2	55	1.14
4453356--4453383	2	14.0	2	100	0	56	50	0	0	50	1.00
4455197--4455248	17	2.8	18	74	11	52	40	0	0	59	0.97
4455404--4455437	2	17.0	2	100	0	68	50	0	0	50	1.00
4460136--4460199	20	3.2	20	64	24	53	40	14	1	43	1.54
4460132--4460212	40	2.0	40	95	0	144	39	16	2	41	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4463223--4463404	81	2.2	83	86	2	242	14	16	47	20	1.82
4463352--4463461	51	2.2	51	86	3	150	15	16	47	20	1.83
4464995--4465047	22	2.4	24	78	18	69	37	5	0	56	1.23
4465027--4465063	17	2.2	17	90	0	56	37	13	0	48	1.43
4468450--4468491	22	1.9	22	90	9	68	61	0	0	38	0.96
4469097--4469151	18	2.9	19	75	15	53	41	0	0	58	0.98
4469071--4469156	40	2.2	39	80	17	99	38	1	1	59	1.13
4470315--4470353	2	19.5	2	100	0	78	51	0	0	48	1.00
4472597--4472630	14	2.3	15	90	5	52	47	2	0	50	1.16
4472803--4472874	11	6.3	11	73	13	56	58	0	0	41	0.98
4474770--4475057	158	1.9	154	87	6	429	39	7	12	40	1.70
4476519--4476557	2	20.0	2	94	5	71	51	0	0	48	1.00
4477829--4477867	18	2.2	19	90	9	64	12	5	0	82	0.83
4477836--4477876	18	2.3	18	82	0	55	19	7	0	73	1.07
4477886--4477939	24	2.2	24	86	0	72	53	1	1	42	1.22
4483539--4483580	21	1.9	23	85	9	61	45	0	0	54	0.99
4484063--4484103	9	4.7	9	80	14	50	36	0	0	63	0.95
4484067--4484107	18	2.3	18	95	0	73	36	0	0	63	0.95
4484063--4484114	26	2.0	26	88	3	77	36	0	0	63	0.95
4484076--4484114	9	4.4	9	81	18	55	35	0	0	64	0.94
4485049--4485092	21	2.1	21	87	4	63	59	0	0	40	0.98
4485042--4485102	29	2.1	30	79	14	74	59	0	0	40	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4485019--4485103	23	3.7	23	70	17	70	57	0	0	42	0.98
4488738--4488782	20	2.1	22	84	8	58	42	2	0	55	1.12
4488740--4488787	20	2.4	20	79	6	53	41	2	0	56	1.11
4492605--4492671	16	4.2	17	69	17	54	41	1	0	56	1.08
4492849--4492910	28	2.3	27	86	8	83	51	1	3	43	1.27
4496232--4496339	46	2.3	46	73	17	116	34	0	3	62	1.13
4496354--4496402	22	2.1	23	88	11	73	32	6	4	57	1.42
4496413--4496457	23	2.0	23	86	0	63	37	8	6	46	1.61
4496761--4496794	17	2.0	17	94	0	59	67	0	8	23	1.18
4499701--4499760	1	60.0	1	79	0	57	0	6	5	88	0.63

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