genome.fa.s25.2.7.7.80.10.50.1000.25.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: 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  25  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)
4330475--4330499	2	12.5	2	100	0	50	48	0	0	52	1.00
4331139--4331164	13	2.0	13	100	0	52	30	15	15	38	1.88
4331203--4331252	25	2.0	25	88	7	75	24	14	16	46	1.83
4331226--4331299	20	3.8	20	85	10	100	28	17	13	40	1.87
4331226--4331273	18	2.6	18	93	6	78	25	18	16	39	1.91
4332497--4332673	51	3.5	50	81	6	196	27	28	11	33	1.91
4332610--4332879	76	3.5	75	86	3	342	27	27	12	32	1.93
4332840--4332955	51	2.3	51	83	7	146	31	24	11	33	1.90
4332804--4333143	157	2.2	156	80	7	366	27	25	12	33	1.93
4332942--4333012	27	2.6	27	84	6	90	23	32	16	26	1.96
4332996--4333115	51	2.4	51	83	5	145	30	24	12	33	1.92
4332966--4333301	129	2.6	126	74	11	311	27	24	12	35	1.91
4338895--4338941	6	7.7	6	88	7	51	76	0	0	23	0.78
4338902--4338941	15	2.7	15	80	11	55	77	0	0	22	0.77
4338931--4339203	35	7.9	35	92	1	433	45	5	28	20	1.73
4339006--4339035	14	2.2	13	94	5	51	40	6	33	20	1.78
4339082--4339138	14	3.7	14	75	20	60	36	7	36	19	1.79
4338931--4339203	103	2.6	105	92	1	442	45	5	28	20	1.73
4340605--4341194	79	7.4	79	90	0	885	27	26	13	31	1.94
4343545--4343676	38	3.5	38	83	4	151	33	19	18	28	1.95
4346170--4346226	23	2.5	23	100	0	114	63	8	10	17	1.51
4347131--4347208	20	3.9	19	80	6	84	41	14	11	33	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4347131--4347208	40	2.0	39	84	2	102	41	14	11	33	1.81
4349081--4349111	2	15.5	2	100	0	62	0	48	0	51	1.00
4350072--4350123	18	2.8	18	76	2	50	38	3	1	55	1.29
4350151--4350195	3	15.0	3	95	0	81	33	0	2	64	1.06
4350214--4350251	20	1.9	20	89	10	60	39	2	2	55	1.28
4350241--4350298	22	2.6	22	77	2	62	24	6	3	65	1.33
4350497--4350530	3	11.7	3	87	6	52	35	2	0	61	1.11
4350587--4350630	20	2.4	18	82	17	63	34	2	0	63	1.07
4350593--4350632	20	2.0	20	95	4	73	32	5	0	62	1.17
4350623--4350673	22	2.4	22	80	9	61	19	7	1	70	1.21
4350662--4350727	21	3.1	21	80	10	64	30	4	4	60	1.37
4350662--4350743	17	4.5	17	75	20	60	29	4	4	60	1.38
4350704--4350776	13	5.2	13	78	18	56	35	4	6	53	1.47
4350698--4350763	31	2.1	31	94	0	114	33	4	6	56	1.44
4350698--4350749	17	3.2	17	75	25	67	30	5	5	57	1.46
4350715--4350756	18	2.3	18	84	8	59	33	4	4	57	1.41
4350711--4350776	22	3.0	22	71	10	62	36	3	7	53	1.45
4350740--4350780	13	3.1	13	93	6	73	43	0	7	48	1.30
4350825--4350881	16	3.4	17	80	11	55	47	0	7	45	1.30
4350842--4350882	18	2.1	19	86	13	57	46	0	9	43	1.36
4353668--4353700	17	1.9	17	100	0	66	36	9	36	18	1.82
4359784--4359808	10	2.5	10	100	0	50	20	0	0	80	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4359843--4359901	18	2.9	20	78	17	68	57	1	1	38	1.19
4359852--4359891	18	2.2	18	95	0	71	60	0	0	40	0.97
4361511--4361542	16	1.9	17	93	6	57	40	0	0	59	0.97
4362462--4362539	29	2.7	30	73	25	78	41	8	6	43	1.62
4362587--4362628	15	2.7	15	82	17	50	26	0	0	73	0.83
4362587--4362628	8	5.2	8	81	18	52	26	0	0	73	0.83
4362860--4362891	8	3.9	8	95	4	55	87	0	9	3	0.64
4365015--4365053	8	4.6	8	81	12	51	84	0	2	12	0.72
4365016--4365053	13	2.9	13	81	14	51	84	0	2	13	0.73
4368658--4368890	60	3.9	60	74	7	163	17	16	16	49	1.80
4368760--4368914	60	2.6	60	79	4	152	18	16	18	46	1.84
4368937--4369099	59	2.8	59	76	1	175	15	10	18	55	1.69
4381519--4381557	19	2.0	20	85	14	55	71	0	12	15	1.14
4381748--4381818	21	3.5	20	75	12	74	46	1	4	47	1.30
4383680--4383730	20	2.5	20	77	0	57	35	9	13	41	1.78
4383774--4383835	20	3.2	19	84	6	70	37	12	9	40	1.77
4383669--4383871	90	2.2	91	88	0	300	31	16	10	41	1.82
4389394--4389444	19	2.7	18	74	11	57	74	7	11	5	1.21
4389355--4389456	45	2.3	45	83	10	120	70	8	11	8	1.34
4389356--4389457	46	2.2	46	81	11	122	69	8	12	8	1.36
4390686--4391033	27	12.7	27	87	1	444	24	32	14	29	1.94
4390686--4391033	55	6.4	54	85	2	426	24	32	14	29	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4390679--4391033	82	4.3	82	89	1	496	23	32	13	29	1.94
4391096--4391203	32	3.5	31	86	7	141	32	27	18	21	1.97
4390652--4391802	28	39.8	29	81	8	731	28	30	15	25	1.96
4391096--4391571	29	15.8	32	75	10	172	31	29	16	22	1.96
4391901--4392071	49	3.6	49	80	4	163	23	27	17	31	1.97
4392794--4392865	20	3.6	20	82	0	90	31	15	13	38	1.87
4392882--4392937	20	2.8	20	83	5	69	32	14	14	39	1.86
4392811--4392965	71	2.2	71	96	1	285	28	17	14	39	1.89
4396600--4396626	2	13.5	2	100	0	54	0	48	0	51	1.00
4397892--4397956	19	3.4	18	69	27	53	52	0	0	47	1.00
4397882--4397957	41	2.0	39	82	14	97	53	0	0	46	1.00
4398286--4398343	24	2.5	23	81	13	66	32	0	0	67	0.91
4398309--4398351	16	2.8	16	82	10	54	32	0	0	67	0.91
4398344--4398387	20	2.2	20	84	4	54	50	4	4	40	1.43
4400532--4400560	14	2.1	14	100	0	58	24	0	20	55	1.44
4400630--4400675	22	2.1	22	88	8	67	54	0	0	45	0.99
4400781--4400836	2	28.0	2	82	7	60	46	3	5	44	1.43
4400770--4400828	20	3.0	20	85	5	75	47	5	6	40	1.52
4400770--4400806	18	1.9	19	89	10	58	48	8	8	35	1.62
4400960--4400998	14	2.7	14	84	15	53	58	7	2	30	1.39
4401233--4401302	37	1.9	36	83	13	90	15	4	8	71	1.26
4404073--4404105	10	3.2	11	87	12	52	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4405334--4405377	23	2.0	22	83	12	56	45	0	0	54	0.99
4409021--4409306	154	1.9	155	80	3	344	30	15	16	38	1.89
4411149--4411310	60	2.7	60	85	4	213	15	15	20	48	1.81
4411143--4411364	60	3.7	59	79	6	207	18	16	18	46	1.84
4411149--4411364	120	1.8	119	82	7	276	17	16	18	46	1.84
4412395--4412629	63	3.7	63	75	8	210	22	21	14	42	1.88
4412576--4412743	62	2.7	61	79	4	167	25	24	11	39	1.88
4412436--4412662	126	1.8	126	80	9	275	21	21	14	42	1.88
4412793--4412913	63	1.9	63	81	1	145	23	14	14	47	1.80
4412885--4412994	32	3.5	31	73	12	107	23	12	8	55	1.64
4412897--4412994	31	3.1	32	75	5	101	22	11	9	57	1.62
4412856--4413054	62	3.2	61	75	5	175	25	14	8	51	1.71
4415104--4415136	9	3.8	9	92	4	50	75	0	0	24	0.80
4424654--4424712	14	4.3	14	77	14	52	54	0	1	44	1.10
4424699--4424742	17	2.6	17	85	0	52	56	2	2	38	1.24
4424669--4424761	47	2.0	46	83	6	116	56	1	3	38	1.22
4425108--4425178	24	2.9	25	81	4	65	52	0	2	45	1.15
4430187--4430225	19	2.0	21	90	10	64	30	12	12	43	1.81
4436919--4436955	10	3.7	10	96	0	65	32	0	8	59	1.27
4437053--4437097	22	2.1	21	87	4	63	57	0	0	42	0.98
4437114--4437167	19	2.7	20	80	16	58	35	0	0	64	0.94
4437145--4437205	30	2.0	31	87	6	90	37	0	0	62	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4437145--4437197	15	3.6	15	72	27	51	37	0	0	62	0.96
4441741--4441786	14	3.1	14	82	11	56	15	4	4	76	1.11
4442601--4442639	20	2.0	20	84	0	51	25	7	0	66	1.18
4442835--4442884	2	25.0	2	100	0	100	50	0	0	50	1.00
4443819--4443894	40	1.9	40	94	0	134	50	9	10	30	1.68
4444589--4444620	16	1.9	17	93	6	57	40	0	0	59	0.97
4445479--4445545	18	3.3	18	67	25	53	22	0	8	68	1.17
4445477--4445563	43	2.0	43	97	0	165	22	0	10	66	1.22
4445480--4445578	43	2.3	43	91	0	144	23	0	12	64	1.27
4447746--4447772	11	2.5	11	100	0	54	81	0	0	18	0.69

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