genome.fa.s64.2.7.7.80.10.50.1000.25.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: 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  25  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)
4495367--4495423	23	2.5	23	82	2	71	45	0	1	52	1.11
4496522--4496620	50	2.0	49	88	5	146	29	4	5	61	1.35
4497493--4497530	7	5.1	7	87	12	58	42	0	0	57	0.98
4497493--4497534	15	2.8	16	89	10	63	47	0	0	52	1.00
4497522--4497573	24	2.2	24	89	6	79	55	1	0	42	1.10
4497839--4497900	3	19.7	3	83	9	79	29	1	3	66	1.17
4498815--4498854	21	1.9	21	89	0	62	30	17	7	45	1.76
4503319--4503375	23	2.5	23	78	13	64	49	0	0	50	1.00
4504324--4504426	46	2.2	46	84	3	127	35	14	10	38	1.81
4506310--4506472	83	2.0	83	97	0	308	28	7	28	34	1.84
4511800--4512085	148	1.9	148	83	2	369	34	14	21	29	1.93
4512857--4512919	16	3.9	16	91	0	99	42	0	3	53	1.16
4512891--4512963	22	3.4	21	69	17	60	43	0	9	46	1.36
4512841--4512920	16	4.8	16	85	4	97	43	0	5	51	1.23
4512898--4512988	43	2.1	43	81	4	103	45	0	9	45	1.37
4513249--4513307	29	2.0	30	80	9	68	50	0	8	40	1.33
4513249--4513310	30	2.1	30	81	6	72	51	0	8	40	1.31
4513288--4513353	21	3.0	22	84	8	80	62	0	3	34	1.11
4513372--4513437	8	7.8	8	73	18	53	59	4	0	36	1.18
4513415--4513453	19	2.2	17	86	9	51	61	2	2	33	1.23
4517308--4517340	2	17.0	2	93	6	59	48	0	0	51	1.00
4518804--4518847	20	2.3	19	88	4	61	27	4	6	61	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4518812--4518921	19	5.8	19	65	11	64	31	6	3	58	1.41
4522966--4523003	17	2.2	17	86	13	51	47	5	0	47	1.24
4523179--4523213	16	2.2	16	94	0	61	0	20	0	80	0.72
4523180--4523214	4	9.0	4	87	6	54	0	22	0	77	0.78
4523311--4523420	20	5.4	20	71	18	77	62	0	0	36	1.01
4523311--4523344	11	3.2	11	83	8	52	70	0	0	29	0.87
4523323--4523452	60	2.3	58	79	14	144	57	0	0	41	1.04
4523385--4523449	10	7.2	9	77	10	62	55	0	0	44	0.99
4523394--4523452	17	3.4	17	88	2	82	55	0	0	44	0.99
4524896--4524943	21	2.3	21	81	0	60	58	6	4	31	1.42
4524959--4525029	31	2.3	30	83	9	81	66	1	0	32	1.01
4524938--4525036	51	2.0	47	81	11	110	65	2	0	32	1.04
4525039--4525108	25	2.7	26	78	6	72	0	27	1	71	0.94
4525055--4525093	17	2.2	18	86	4	53	0	28	2	69	1.02
4526014--4526046	2	16.5	2	100	0	66	51	0	0	48	1.00
4529043--4529190	80	1.9	80	88	0	224	30	20	14	34	1.92
4541634--4541662	2	14.5	2	100	0	58	51	0	0	48	1.00
4542013--4542072	24	2.3	26	83	8	70	38	1	6	53	1.37
4541992--4542171	63	2.8	65	75	17	182	40	1	2	56	1.19
4542286--4542325	21	1.9	21	84	0	53	37	10	2	50	1.50
4544331--4544390	24	2.7	22	80	17	54	56	0	1	41	1.09
4544712--4544755	15	2.8	17	74	25	51	43	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4544767--4544800	13	2.4	14	85	14	52	67	0	0	32	0.91
4544774--4544800	13	2.1	13	100	0	54	70	0	0	29	0.88
4557563--4557676	32	3.6	33	74	14	105	42	1	1	54	1.21
4557634--4557699	33	2.0	32	82	2	78	45	0	0	54	0.99
4557665--4557726	23	2.7	24	85	7	83	37	0	0	62	0.95
4557657--4557727	18	3.9	18	76	9	65	36	0	0	63	0.95
4559550--4559615	24	2.7	25	71	17	66	42	1	0	56	1.08
4559797--4559829	16	2.1	16	94	0	57	48	24	15	12	1.78
4561834--4561875	18	2.3	19	91	4	68	90	4	2	2	0.60
4563124--4563201	25	3.1	26	78	16	92	34	0	1	64	1.02
4563126--4563197	18	4.2	17	72	16	60	33	0	1	65	1.02
4564980--4565022	2	21.5	2	100	0	86	51	0	0	48	1.00
4565322--4565363	3	14.0	3	100	0	84	66	0	0	33	0.92
4565596--4565621	3	8.7	3	100	0	52	69	0	0	30	0.89
4566915--4566984	21	3.3	20	69	15	61	55	1	7	35	1.36
4566912--4566991	42	1.9	42	97	0	151	52	2	7	37	1.43
4566927--4566993	21	3.2	21	65	23	59	52	2	5	38	1.41
4567127--4567175	26	2.0	25	84	8	64	30	8	2	59	1.38
4570103--4570129	14	1.9	14	100	0	54	51	0	33	14	1.43
4573426--4574199	49	15.5	49	81	4	809	33	17	25	23	1.96
4573426--4574199	101	7.8	98	86	3	818	33	17	25	23	1.96
4573517--4574199	153	4.6	149	83	4	806	33	18	25	23	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4574207--4574322	27	4.0	27	79	14	124	33	12	31	21	1.91
4574235--4574477	34	7.6	34	75	15	207	39	12	27	20	1.89
4574219--4574356	61	2.3	61	93	0	231	38	11	28	21	1.88
4574249--4574463	95	2.3	95	88	1	326	42	12	26	19	1.86
4574425--4574696	32	8.7	31	82	8	295	34	15	27	22	1.94
4574450--4574697	30	8.0	30	82	8	275	34	15	27	22	1.94
4574417--4574709	62	4.7	62	85	4	365	36	14	27	21	1.92
4574425--4574696	126	2.2	124	87	2	375	34	15	27	22	1.94
4574838--4574876	16	2.3	18	83	16	57	28	12	7	51	1.67
4577535--4577587	20	2.7	20	82	5	63	41	11	15	32	1.82
4577619--4577681	19	3.6	19	76	24	84	34	19	12	33	1.89
4577613--4577681	32	2.2	32	100	0	138	36	18	11	33	1.87
4577638--4577662	13	1.9	13	100	0	50	32	16	16	36	1.90
4584074--4584148	36	2.1	36	82	0	87	34	18	8	38	1.80
4587138--4587182	19	2.4	19	81	7	56	51	2	0	46	1.13
4589339--4589363	12	2.1	12	100	0	50	32	28	0	40	1.57
4593948--4593973	3	8.7	3	100	0	52	34	65	0	0	0.93
4597963--4597987	7	3.6	7	100	0	50	12	0	0	88	0.53
4599869--4599906	6	6.5	6	96	3	69	47	18	34	0	1.49
4600511--4600561	19	2.7	19	85	11	77	64	0	0	35	0.94
4601734--4601783	25	2.0	25	100	0	100	28	16	20	36	1.93
4607855--4607930	29	2.5	30	81	10	84	30	7	5	56	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4608138--4608177	18	2.2	19	90	4	64	60	2	2	35	1.24
4609083--4609149	19	3.5	19	70	15	57	58	1	0	40	1.07
4614518--4614568	19	2.6	19	79	11	59	50	0	1	47	1.12
4616651--4616716	18	3.6	18	76	13	64	31	0	0	68	0.90
4616621--4616689	27	2.6	27	82	13	74	34	0	1	63	1.03
4616650--4616772	21	5.4	21	67	27	65	30	1	2	65	1.15
4616624--4616785	67	2.5	66	72	11	154	32	1	3	63	1.17
4616649--4616703	27	2.0	27	82	6	67	36	0	0	63	0.95
4616743--4616785	12	3.7	12	81	6	52	30	0	4	65	1.13
4617251--4617316	11	5.9	11	77	8	62	37	3	0	59	1.13
4617443--4617513	16	4.4	16	71	13	56	33	4	1	60	1.25
4617718--4617748	16	1.9	16	93	0	53	74	3	0	22	0.96
4618291--4618348	25	2.3	25	77	11	64	55	0	1	43	1.10
4618820--4618877	22	2.6	24	78	15	70	50	0	0	50	1.00
4620000--4620032	2	16.5	2	100	0	66	51	0	0	48	1.00
4620362--4620393	2	16.0	2	100	0	64	50	0	0	50	1.00
4621478--4621569	34	2.7	34	84	1	112	38	35	2	23	1.67
4623227--4623262	17	2.1	17	89	0	54	13	11	0	75	1.06
4626319--4626369	22	2.3	23	93	3	86	37	27	3	31	1.75
4629598--4629642	2	22.5	2	100	0	90	51	0	0	48	1.00
4631022--4631070	6	7.8	6	82	8	62	38	0	0	61	0.96
4632276--4632339	32	2.0	33	84	9	87	43	1	1	53	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4633161--4633197	18	2.1	18	100	0	74	43	16	8	32	1.77
4634458--4634506	2	24.5	2	95	0	89	48	0	2	48	1.12
4634667--4634713	2	23.0	2	95	4	85	48	2	0	48	1.13
4635036--4635087	2	26.0	2	92	0	86	46	0	3	50	1.20
4635574--4635657	6	14.3	6	81	10	68	54	1	0	44	1.07
4641438--4641490	6	8.8	6	91	0	70	39	49	9	1	1.46
4641431--4641492	18	3.4	18	84	2	79	41	46	8	3	1.49
4643606--4643672	33	2.1	32	97	2	125	26	19	17	35	1.94
4645220--4645244	2	12.5	2	100	0	50	48	52	0	0	1.00
4648596--4648624	3	9.7	3	100	0	58	0	31	0	68	0.89

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