genome.fa.s25.2.7.7.80.10.50.1000.24.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  24  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)
4206932--4206973	17	2.4	18	80	15	52	57	0	0	42	0.99
4207018--4207053	11	3.2	11	88	7	54	50	0	8	41	1.33
4207411--4207451	21	2.0	21	85	9	57	68	4	0	26	1.10
4207755--4207785	16	1.9	16	93	0	53	54	0	9	35	1.33
4208826--4208903	26	3.1	25	71	25	74	44	0	0	55	0.99
4209250--4209346	47	2.1	46	83	16	121	39	0	1	59	1.04
4209252--4209318	27	2.4	28	74	16	68	41	0	0	58	0.98
4209283--4209326	20	2.2	20	84	8	54	38	0	2	59	1.10
4209278--4209357	32	2.5	31	76	6	88	35	0	1	63	1.02
4209328--4209427	21	4.7	20	69	20	60	32	1	1	66	1.05
4209335--4209409	16	4.3	18	68	19	59	28	1	1	69	1.05
4209335--4209387	24	2.3	23	84	12	72	26	1	1	69	1.09
4209334--4209426	29	3.3	26	78	15	80	31	1	1	66	1.05
4209245--4209427	11	15.8	12	68	18	79	36	0	1	62	1.07
4209399--4209423	13	1.9	13	100	0	50	44	0	0	56	0.99
4209418--4209471	23	2.2	24	84	12	67	46	3	1	48	1.30
4210061--4210100	21	1.9	21	84	0	53	57	0	0	42	0.98
4210127--4210178	12	4.2	12	73	9	50	51	0	0	48	1.00
4210789--4210917	18	7.1	18	68	19	56	60	0	0	39	0.97
4210804--4210850	16	3.0	16	82	14	62	61	0	0	38	0.96
4210795--4210869	19	3.8	20	75	18	77	61	0	0	38	0.96
4210782--4210856	22	3.4	24	77	15	72	62	0	1	36	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4210826--4210911	32	2.6	32	87	5	109	56	0	0	43	0.99
4211156--4211215	11	5.5	11	77	15	54	28	0	1	70	0.97
4211616--4211665	26	1.9	26	84	8	66	44	0	2	54	1.11
4211899--4211947	20	2.5	20	86	3	64	44	2	0	53	1.12
4212333--4212367	14	2.5	14	90	9	54	45	0	0	54	0.99
4212373--4212440	22	2.9	22	79	20	68	60	0	0	39	0.97
4212384--4212457	22	3.3	22	78	14	71	59	0	0	40	0.97
4212373--4212440	11	5.9	12	71	20	56	60	0	0	39	0.97
4212385--4212438	15	3.5	15	76	2	54	62	0	0	37	0.95
4212373--4212457	33	2.5	35	78	17	92	58	0	0	41	0.98
4212970--4213019	19	2.4	20	80	16	57	46	2	0	52	1.12
4213264--4213325	27	2.3	26	76	13	63	38	1	1	58	1.18
4213367--4213425	19	2.9	19	75	20	57	55	1	0	42	1.09
4213372--4213447	23	3.3	24	80	8	88	59	1	0	39	1.06
4216178--4216213	2	18.0	2	100	0	72	0	50	0	50	1.00
4216619--4216654	17	2.2	16	90	5	54	41	0	2	55	1.14
4216611--4216660	23	2.2	23	85	7	66	46	0	2	52	1.12
4219245--4219324	22	3.8	21	75	12	67	55	0	1	43	1.08
4220322--4220359	16	2.4	16	86	8	51	50	15	13	21	1.78
4228386--4228574	37	5.0	37	79	7	184	35	18	19	26	1.95
4232036--4232100	33	2.0	32	82	11	80	44	4	4	46	1.44
4232551--4232591	13	3.0	14	82	13	50	63	0	7	29	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4232596--4232632	2	19.0	2	94	5	67	51	0	0	48	1.00
4233962--4234003	2	21.0	2	85	0	57	50	7	0	42	1.30
4233962--4234004	12	3.6	12	90	0	68	48	9	0	41	1.35
4234305--4234339	2	17.5	2	93	0	61	48	0	2	48	1.16
4234643--4234677	2	17.5	2	100	0	70	48	0	0	51	1.00
4235489--4235533	18	2.9	15	79	20	56	55	6	0	37	1.26
4235462--4235533	32	2.2	32	82	5	81	56	4	0	38	1.18
4235496--4235539	18	2.3	18	80	7	52	56	6	0	36	1.26
4235809--4235961	19	8.7	18	72	16	54	39	0	0	59	1.07
4235824--4235969	28	5.2	28	71	17	108	39	0	0	59	1.07
4237232--4237296	31	2.0	33	85	5	89	50	1	0	47	1.10
4237231--4237310	33	2.5	33	80	12	85	48	1	0	50	1.08
4244218--4244252	17	2.1	16	89	5	52	45	2	0	51	1.16
4245523--4245611	29	3.0	30	74	12	76	58	3	3	34	1.31
4245969--4246078	2	57.0	2	73	20	74	52	3	3	40	1.36
4245969--4246078	47	2.4	46	96	3	204	52	3	3	40	1.36
4252212--4252264	25	2.0	25	89	7	79	50	0	1	47	1.12
4254492--4254539	18	2.6	19	76	6	53	47	0	0	52	1.00
4255505--4255541	3	12.3	3	100	0	74	32	0	0	67	0.91
4256432--4256459	2	14.0	2	100	0	56	50	0	0	50	1.00
4259681--4259928	132	1.9	132	93	0	424	37	20	15	27	1.93
4261478--4261502	1	25.0	1	100	0	50	100	0	0	0	0.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4263478--4263520	20	2.1	22	83	12	56	62	0	0	37	0.95
4263838--4263882	23	2.0	23	86	0	63	55	0	2	42	1.12
4263912--4263953	16	2.4	18	84	11	52	57	0	2	40	1.12
4263952--4263995	21	2.1	21	91	8	72	54	6	0	38	1.27
4269932--4269972	20	2.1	19	86	4	55	46	0	0	53	1.00
4270689--4270741	27	2.0	26	85	3	70	49	0	0	50	1.00
4271010--4271055	14	3.1	15	75	15	51	50	0	8	41	1.33
4273726--4273752	2	13.5	2	100	0	54	51	0	0	48	1.00
4275345--4275385	2	20.5	2	84	0	55	48	7	0	43	1.30
4275547--4275597	24	2.0	25	82	14	61	45	3	0	50	1.20
4276980--4277027	22	2.2	22	88	0	69	41	0	0	58	0.98
4276989--4277077	42	2.2	39	75	19	92	46	0	0	53	1.00
4277024--4277053	15	2.0	15	100	0	60	46	0	0	53	1.00
4277056--4277110	20	2.9	19	82	15	69	32	0	1	65	1.03
4277006--4277096	43	2.1	43	86	8	123	41	0	0	58	0.98
4277067--4277108	12	3.1	14	80	16	52	30	0	2	66	1.04
4277844--4277897	27	2.0	27	82	3	65	42	0	3	53	1.18
4279208--4279248	21	2.0	21	90	9	66	41	0	0	58	0.98
4279246--4279283	20	1.9	20	88	0	58	50	0	0	50	1.00
4281797--4281830	15	2.4	14	95	5	59	35	0	0	64	0.94
4281805--4281838	15	2.3	15	89	0	50	41	0	0	58	0.98
4281982--4282032	17	3.0	17	76	18	61	58	0	1	39	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4282085--4282141	24	2.5	24	88	5	82	52	0	0	47	1.00
4283086--4283160	30	2.5	30	82	6	89	41	2	1	54	1.23
4283251--4283281	2	15.5	2	93	0	53	51	0	0	48	1.00
4284893--4284947	25	2.2	25	83	0	65	34	10	36	18	1.86
4285022--4285091	27	2.6	26	81	4	77	51	15	7	25	1.69
4286972--4287017	21	2.1	22	84	4	58	19	30	19	30	1.97
4289459--4289504	13	3.6	13	82	5	58	34	6	41	17	1.75
4289583--4289655	27	2.7	27	86	0	110	47	20	6	24	1.74
4291481--4291525	17	2.7	16	81	18	56	66	0	0	33	0.92
4291790--4291821	3	10.7	3	100	0	64	31	0	0	68	0.90
4294672--4294702	2	15.5	2	100	0	62	51	48	0	0	1.00
4295068--4295115	22	2.1	23	88	7	71	47	4	4	43	1.41
4295794--4295854	20	2.7	23	72	25	58	49	1	0	49	1.10
4301963--4302025	10	6.0	10	75	12	56	73	1	1	23	1.01
4303078--4303141	19	3.1	20	82	11	76	40	6	0	53	1.26
4309862--4309917	2	28.0	2	96	0	103	51	0	0	48	1.00
4315446--4315474	3	9.7	3	100	0	58	65	0	0	34	0.93
4315487--4315533	12	3.5	13	77	13	51	46	0	0	53	1.00
4315487--4315536	13	3.8	13	84	5	64	50	0	0	50	1.00
4315672--4315711	13	3.1	13	96	0	71	42	0	0	57	0.98
4315672--4315725	13	4.1	13	90	2	63	38	0	0	61	0.96
4316162--4316199	19	2.0	20	90	10	62	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)
4317857--4317904	18	2.8	18	90	6	73	62	0	0	37	0.95
4317862--4317913	22	2.4	22	77	3	61	67	0	0	32	0.91
4318708--4318770	21	2.7	24	78	16	78	38	7	0	53	1.30
4320375--4320407	10	3.2	11	87	12	52	51	0	0	48	1.00
4321438--4321469	7	4.7	7	96	3	57	21	0	0	78	0.76
4321646--4321689	23	2.0	22	83	12	56	45	0	0	54	0.99
4327314--4327362	24	2.0	24	88	0	71	14	22	14	48	1.79
4327523--4327749	60	3.8	60	77	7	214	17	16	20	45	1.86
4327523--4327776	120	2.1	116	78	9	260	18	16	20	45	1.85
4328962--4329086	63	2.0	63	81	4	146	22	21	14	41	1.89

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