genome.fa.s64.2.7.7.80.10.50.1000.22.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   

This is table  22  of  45  ( 5312 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)
4048938--4048969	13	2.6	13	90	9	50	28	0	0	71	0.86
4054140--4054561	212	2.0	212	93	0	720	24	15	22	37	1.93
4054616--4054679	23	3.0	23	70	25	77	40	6	12	40	1.68
4054638--4054670	17	1.9	17	93	0	57	42	3	12	42	1.57
4054675--4054708	15	2.3	15	89	0	50	50	17	8	23	1.74
4054793--4054854	31	2.0	31	90	0	97	51	11	9	27	1.69
4061036--4061072	18	2.0	18	89	5	56	54	0	0	45	1.00
4061062--4061123	28	2.4	26	82	12	74	46	0	0	53	1.00
4061443--4061486	13	3.1	14	87	9	54	40	0	0	59	0.98
4061446--4061589	29	4.9	29	65	20	84	44	0	0	54	1.10
4061407--4061487	36	2.2	35	84	8	99	38	0	2	59	1.11
4061447--4061517	30	2.4	31	85	7	101	46	0	0	53	1.00
4061447--4061516	14	4.7	14	73	21	54	47	0	0	52	1.00
4061446--4061550	28	3.7	28	74	21	94	46	0	0	52	1.07
4061563--4061600	14	2.6	15	88	12	53	42	0	0	57	0.98
4061553--4061598	13	3.5	13	82	11	51	36	2	0	60	1.09
4063665--4063715	25	2.0	25	81	7	59	50	5	0	43	1.26
4063788--4063858	35	2.0	35	83	5	90	56	2	2	38	1.29
4064915--4064948	6	5.5	6	86	6	50	61	2	0	35	1.11
4064951--4065001	22	2.3	22	89	0	75	41	13	0	45	1.44
4065955--4065996	18	2.3	19	87	4	68	59	0	0	40	0.97
4066616--4066650	3	11.7	3	93	0	61	71	0	0	28	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4077506--4077824	165	1.9	163	96	1	593	33	18	19	28	1.95
4079031--4079075	16	2.8	16	82	0	54	53	0	2	44	1.13
4079162--4079192	16	1.9	16	93	0	53	48	0	3	48	1.17
4079129--4079261	69	1.9	69	87	6	198	50	0	3	45	1.22
4079131--4079240	22	4.9	22	73	11	98	50	0	2	46	1.22
4079209--4079259	16	3.2	16	83	5	59	56	0	0	43	0.99
4079221--4079269	17	2.9	17	84	3	55	57	0	0	42	0.99
4079221--4079280	27	2.3	25	88	5	84	60	0	0	40	0.97
4079241--4079282	8	5.2	8	80	8	50	61	0	0	38	0.96
4079137--4079279	69	2.1	69	83	7	175	53	0	2	44	1.17
4087419--4087448	14	2.1	14	100	0	60	26	36	26	10	1.88
4089423--4089594	95	1.8	94	80	10	208	30	12	14	42	1.83
4089653--4089762	48	2.3	48	80	9	118	44	10	10	35	1.71
4089816--4089867	25	2.1	25	85	0	68	34	13	25	26	1.93
4093314--4093352	19	2.1	19	85	0	51	64	5	30	0	1.15
4097793--4097827	15	2.2	17	90	10	56	11	25	11	51	1.71
4097880--4097911	2	16.0	2	100	0	64	50	0	0	50	1.00
4102079--4102183	47	2.3	44	78	16	106	47	6	4	40	1.51
4102491--4102522	15	2.1	15	94	0	55	50	3	0	46	1.17
4102522--4102696	74	2.4	73	84	5	221	43	4	3	49	1.38
4103228--4103252	12	2.1	12	100	0	50	92	0	8	0	0.40
4109446--4109476	2	15.5	2	100	0	62	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4117299--4117516	34	6.4	34	85	2	287	25	7	25	41	1.81
4117299--4117516	102	2.1	101	93	1	373	25	7	25	41	1.81
4121916--4122134	34	6.5	34	84	4	273	26	7	24	40	1.82
4121916--4122133	102	2.1	101	89	0	328	27	7	24	40	1.82
4122838--4123025	94	2.0	94	93	0	322	38	14	28	18	1.90
4125112--4125157	21	2.2	21	84	7	58	39	0	2	58	1.10
4125230--4125380	7	25.2	6	71	21	61	63	0	0	35	0.99
4125223--4125280	29	1.9	31	89	6	93	67	0	1	31	1.01
4125243--4125387	29	4.9	30	74	15	106	62	0	0	36	1.00
4125330--4125376	17	2.9	17	84	6	53	70	0	0	29	0.88
4126026--4126113	19	4.8	18	76	18	76	54	0	0	45	0.99
4129664--4129721	21	2.7	21	79	12	64	56	0	0	43	0.99
4130537--4130769	120	1.9	120	88	0	349	28	26	18	27	1.98
4131771--4131848	41	1.9	41	94	0	138	46	3	23	26	1.69
4136880--4136963	41	2.1	41	86	2	116	27	14	13	45	1.81
4142199--4142243	2	22.5	2	95	0	81	48	0	2	48	1.13
4145958--4145995	18	2.1	18	85	9	51	26	0	2	71	1.00
4146198--4146256	29	2.0	29	84	12	77	42	0	5	52	1.23
4150188--4150233	20	2.4	19	82	10	58	60	0	0	39	0.97
4152320--4152344	3	8.3	3	100	0	50	32	0	0	68	0.90
4152584--4152633	20	2.5	20	90	0	73	38	2	4	56	1.30
4153308--4153339	4	8.0	4	100	0	64	25	0	0	75	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4153582--4153631	14	3.8	14	76	10	52	38	0	0	62	0.96
4154069--4154127	29	2.2	25	75	18	64	52	1	0	45	1.10
4154744--4154788	23	2.0	23	86	0	63	44	0	2	53	1.13
4155261--4155285	11	2.3	11	100	0	50	40	36	16	8	1.77
4155554--4155606	25	2.0	28	89	10	85	47	1	0	50	1.12
4156695--4156731	2	18.5	2	100	0	74	51	0	0	48	1.00
4158901--4158942	22	1.9	22	90	0	66	47	0	0	52	1.00
4159721--4159770	16	3.1	16	78	16	57	30	0	0	70	0.88
4159708--4159777	21	3.5	19	77	14	61	32	0	0	67	0.91
4160573--4160639	37	1.9	33	82	11	80	46	2	1	49	1.26
4162780--4162857	32	2.4	31	84	14	104	56	0	0	43	0.99
4163915--4163955	17	2.5	17	88	4	57	26	7	0	65	1.18
4163918--4163984	30	2.3	29	82	10	82	29	4	0	65	1.12
4164433--4164509	29	2.6	29	76	11	68	49	5	0	45	1.24
4166423--4166455	17	1.9	17	88	11	50	39	3	3	54	1.31
4173237--4173273	7	4.8	8	90	9	51	0	89	8	2	0.58
4174086--4174129	19	2.3	19	76	0	52	40	6	2	50	1.42
4174818--4174898	11	7.5	11	75	15	62	39	0	0	60	0.97
4174820--4174900	29	2.7	30	79	12	78	38	0	0	61	0.96
4174820--4174873	19	2.8	20	81	13	60	42	0	0	57	0.98
4174828--4174911	18	4.8	17	75	13	64	35	0	0	64	0.94
4174857--4174911	6	9.7	6	75	18	55	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4174848--4174912	29	2.2	28	83	5	76	33	0	0	66	0.92
4174795--4174971	97	1.8	96	80	12	211	39	0	0	59	1.06
4174942--4174980	17	2.3	17	83	12	53	33	2	0	64	1.08
4175233--4175257	13	1.9	13	100	0	50	36	16	16	32	1.90
4175213--4175279	33	2.0	33	88	0	98	32	11	14	40	1.83
4175320--4175344	13	1.9	13	100	0	50	32	16	16	36	1.90
4175333--4175481	52	2.9	52	86	2	210	34	18	16	30	1.92
4178534--4178581	22	2.3	22	83	16	59	31	2	0	66	1.03
4178847--4178911	11	6.1	11	74	13	55	30	3	0	66	1.07
4179110--4179148	20	2.0	20	89	0	60	53	0	0	46	1.00
4179345--4179417	26	2.8	27	80	17	75	47	0	1	50	1.09
4179354--4179404	22	2.4	21	81	15	61	47	0	0	52	1.00
4180872--4180953	36	2.2	37	81	14	98	63	1	1	34	1.10
4180900--4180956	23	2.6	22	83	8	71	68	0	0	31	0.90
4180923--4180955	14	2.3	15	89	5	50	69	0	0	30	0.88
4180934--4181004	28	2.6	27	78	12	74	57	4	4	33	1.37
4181223--4181283	14	4.3	15	69	24	51	45	0	0	54	1.00
4181221--4181285	30	2.3	28	84	7	78	47	0	0	52	1.00
4181218--4181287	28	2.8	24	78	19	79	45	0	0	54	0.99
4182905--4182949	3	15.0	3	100	0	90	66	0	0	33	0.92
4183124--4183156	17	1.9	17	93	0	57	39	0	0	60	0.97
4187951--4187984	2	18.0	2	88	11	54	47	0	52	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4188232--4188322	2	44.5	2	75	8	76	4	45	3	47	1.39
4188772--4188801	2	15.5	2	93	6	53	0	46	0	53	1.00
4189731--4189762	2	16.0	2	93	0	55	0	50	3	46	1.17
4192934--4192969	16	2.2	17	90	5	56	27	0	16	55	1.42
4193367--4193415	13	3.5	14	74	20	57	57	2	0	40	1.10
4193367--4193417	15	3.6	14	79	12	59	56	1	0	41	1.10
4198311--4198367	25	2.4	22	78	16	60	56	0	5	38	1.22
4198627--4198657	16	2.0	16	93	6	55	25	0	0	74	0.82
4198968--4199023	22	2.5	23	79	5	69	57	3	5	33	1.39
4199223--4199265	2	21.5	2	100	0	86	48	0	0	51	1.00

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