genome.fa.s25.2.7.7.80.10.50.1000.23.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  23  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)
4062694--4062743	23	2.3	22	86	10	68	66	0	2	32	1.03
4062709--4062773	28	2.3	29	82	10	73	64	0	1	33	1.03
4062694--4062777	11	8.3	11	76	16	67	65	0	1	33	1.00
4062725--4062769	17	2.6	18	77	22	51	62	0	2	35	1.08
4062716--4062904	104	1.8	104	83	8	251	59	2	2	35	1.23
4062902--4062965	10	6.5	10	75	10	69	68	0	0	31	0.90
4062900--4063002	27	3.8	25	71	14	71	66	0	0	32	0.98
4065801--4065865	17	3.9	16	74	6	58	55	1	0	43	1.09
4068723--4068748	2	13.0	2	100	0	52	0	50	0	50	1.00
4077468--4077549	30	2.7	30	83	3	85	28	21	12	37	1.90
4077610--4077685	30	2.5	30	76	0	80	19	18	21	40	1.91
4077503--4077696	107	1.8	107	81	2	246	24	18	19	38	1.93
4079181--4079252	28	2.6	28	86	4	92	22	19	36	22	1.95
4079240--4079410	51	3.3	51	82	5	209	32	11	25	29	1.91
4079393--4079468	27	2.8	28	89	2	109	21	21	34	23	1.97
4081865--4081891	13	2.1	13	100	0	54	40	14	14	29	1.86
4081931--4081998	19	3.9	18	76	23	83	38	14	11	35	1.83
4081953--4081977	13	1.9	13	100	0	50	32	16	16	36	1.90
4081934--4081996	32	2.0	32	96	0	117	36	15	12	34	1.86
4082034--4082090	21	2.7	22	89	8	91	35	15	10	38	1.82
4086159--4086210	19	2.6	21	84	6	72	38	11	15	34	1.83
4086263--4086288	13	2.0	13	100	0	52	30	15	15	38	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4088665--4088778	51	2.3	48	82	10	140	27	25	12	35	1.91
4088713--4089087	79	4.8	79	81	4	406	28	24	13	33	1.94
4089021--4089189	51	3.3	51	93	0	275	27	24	14	33	1.94
4089124--4089309	79	2.4	79	85	2	248	25	25	15	33	1.95
4089125--4089350	79	2.9	79	83	4	242	26	24	14	34	1.94
4091487--4091511	4	6.2	4	100	0	50	24	0	0	76	0.80
4093645--4093719	20	3.8	20	78	0	87	34	13	12	40	1.81
4093645--4093722	40	2.0	39	87	2	111	34	12	12	39	1.82
4094630--4094681	22	2.3	23	93	6	97	19	11	9	59	1.59
4098000--4098030	4	7.8	4	100	0	62	22	0	0	77	0.77
4107755--4107804	26	2.0	25	96	4	91	86	14	0	0	0.58
4107757--4107804	13	3.7	13	88	0	78	89	10	0	0	0.48
4107757--4107811	1	55.0	1	81	0	56	89	9	1	0	0.57
4109038--4110603	29	54.9	29	91	3	2341	28	32	17	21	1.96
4109040--4110615	86	18.4	86	90	3	2366	28	32	17	21	1.96
4111129--4111203	20	3.8	20	78	0	87	34	13	12	40	1.81
4111129--4111206	40	2.0	39	87	2	111	34	12	12	39	1.82
4112114--4112165	22	2.3	23	93	6	97	19	11	9	59	1.59
4117605--4117678	23	3.2	21	75	17	67	39	1	0	59	1.06
4117608--4117665	10	5.2	11	77	18	50	41	1	0	56	1.09
4118682--4118807	11	11.6	11	67	18	68	57	1	0	40	1.08
4118689--4118731	19	2.2	20	87	4	61	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4118702--4118768	16	4.2	16	73	21	52	56	0	0	43	0.99
4119082--4119158	12	6.9	12	72	19	51	54	0	1	44	1.08
4119082--4119132	13	4.2	13	76	19	56	56	0	0	43	0.99
4119086--4119139	22	2.5	22	81	6	56	57	0	0	42	0.98
4119972--4120013	20	2.2	19	87	12	59	64	0	0	35	0.94
4120440--4120490	3	17.0	3	100	0	102	33	0	0	66	0.92
4122825--4122880	21	2.6	21	78	13	60	62	0	1	35	1.06
4122843--4122897	25	2.1	25	83	12	67	63	3	0	32	1.12
4130095--4131211	262	4.0	283	82	9	1349	43	15	16	23	1.87
4132532--4132588	11	4.9	11	81	10	60	54	0	0	45	0.99
4132545--4132577	13	2.3	15	85	15	52	51	0	0	48	1.00
4132532--4132577	24	2.0	23	91	4	74	50	0	0	50	1.00
4132521--4132588	35	1.9	36	82	8	86	52	0	0	47	1.00
4135473--4135556	40	2.1	41	88	2	125	66	4	1	27	1.19
4138977--4139003	10	2.7	10	100	0	54	92	0	7	0	0.38
4140053--4140089	5	7.4	5	87	0	56	51	0	0	48	1.00
4140368--4140413	21	2.3	19	82	17	58	26	8	0	65	1.21
4140567--4140637	26	2.8	25	76	4	70	47	2	0	49	1.16
4142311--4142340	15	2.1	15	93	6	53	63	0	3	33	1.11
4142735--4142785	15	3.8	13	80	14	50	50	13	3	31	1.60
4142749--4142785	15	2.7	14	88	12	51	54	13	2	29	1.53
4145386--4145438	22	2.5	21	76	11	54	47	0	1	50	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4145388--4145433	22	2.1	22	84	8	58	43	0	2	54	1.12
4146327--4146374	17	2.9	15	77	19	51	47	0	0	52	1.00
4149214--4149288	20	3.8	20	78	0	87	34	13	12	40	1.81
4149214--4149291	40	2.0	39	87	2	111	34	12	12	39	1.82
4150201--4150251	21	2.3	22	90	10	86	19	11	9	58	1.60
4150212--4150256	21	2.2	21	80	11	58	22	8	8	60	1.55
4153571--4153601	4	7.8	4	100	0	62	22	0	0	77	0.77
4163329--4163375	13	3.6	13	88	0	76	89	10	0	0	0.49
4163329--4163382	1	54.0	1	81	0	54	88	9	1	0	0.58
4164611--4166182	29	54.9	29	92	2	2384	28	32	17	21	1.96
4164613--4166194	86	18.4	86	90	2	2409	28	32	17	21	1.96
4164613--4166194	601	2.6	601	95	1	2789	28	32	17	21	1.96
4166708--4166782	20	3.8	20	78	0	87	34	13	12	40	1.81
4166708--4166785	40	2.0	39	87	2	111	34	12	12	39	1.82
4167693--4167744	22	2.3	23	93	6	97	19	11	9	59	1.59
4178378--4178433	8	7.0	8	84	12	71	83	12	3	0	0.76
4178389--4178428	7	5.4	7	82	11	53	87	12	0	0	0.54
4178380--4178428	15	3.2	15	91	8	73	85	12	2	0	0.68
4178378--4178433	23	2.3	23	88	11	78	83	12	3	0	0.76
4178379--4178434	15	3.2	18	80	14	64	85	10	3	0	0.71
4179501--4180092	55	10.3	55	82	10	602	27	26	20	26	1.99
4179698--4179783	27	3.1	27	62	15	68	27	23	18	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4179780--4179865	27	3.1	27	64	15	68	25	23	20	30	1.99
4179501--4180092	116	5.1	116	84	8	694	27	26	20	26	1.99
4179497--4180372	171	5.1	169	79	11	807	26	26	19	27	1.99
4180137--4180372	61	3.9	61	83	6	284	24	27	21	26	1.99
4180143--4180364	122	1.8	122	89	2	349	24	28	21	26	1.99
4179907--4180303	215	1.8	215	86	5	570	25	27	19	26	1.99
4181217--4181266	19	2.5	21	87	6	68	42	14	12	32	1.82
4181296--4181353	21	2.8	21	100	0	116	34	10	17	37	1.84
4181340--4181365	13	2.0	13	100	0	52	30	15	15	38	1.88
4183777--4184154	79	4.8	79	81	5	378	28	25	12	32	1.93
4184091--4184260	51	3.3	51	92	0	268	27	25	14	31	1.95
4184242--4184314	28	2.6	27	87	8	94	23	32	19	24	1.97
4186027--4186125	52	1.9	52	83	4	128	8	18	25	48	1.75
4186073--4186315	61	4.0	61	86	2	272	7	17	27	47	1.75
4186226--4186340	61	2.0	57	83	10	144	5	21	31	41	1.75
4186533--4186604	36	2.0	35	81	2	81	19	12	31	36	1.89
4186543--4186610	35	1.9	36	85	5	95	19	11	29	39	1.87
4187000--4187075	7	10.4	7	78	10	55	18	2	3	75	1.08
4187001--4187055	22	2.6	21	85	5	76	18	1	3	76	1.02
4187551--4188040	42	11.6	41	76	8	303	34	18	28	17	1.94
4187551--4188129	85	6.8	85	79	7	430	34	18	29	17	1.94
4187585--4188128	170	3.2	168	78	7	514	34	18	28	17	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4187798--4188125	42	7.7	42	79	8	299	35	19	28	15	1.93
4187585--4188128	43	12.8	43	74	7	387	34	18	28	17	1.94
4192551--4192849	61	4.8	61	78	4	278	6	19	27	45	1.75
4193020--4193088	36	1.9	35	85	2	93	18	11	30	39	1.87
4193489--4193550	22	2.8	21	79	18	72	22	1	3	72	1.08
4196510--4196572	28	2.2	29	83	8	76	39	3	3	53	1.33
4196839--4196876	17	2.2	18	85	4	51	7	18	10	63	1.50
4200439--4200525	15	5.6	16	75	15	76	43	6	4	44	1.51
4200530--4200561	15	2.1	15	94	0	55	40	6	12	40	1.68
4202631--4202859	115	2.0	114	93	0	395	34	24	10	30	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