genome.fa.s63.2.7.7.80.10.50.1000.1.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: Scaffold63
Parameters: 2 7 7 80 10 50 1000
Length:  2211945

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   

This is table  1  of  16  ( 1834 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)
12448--12924	7	69.4	7	76	9	191	4	7	54	33	1.48
12742--12778	19	2.0	19	89	5	58	2	10	62	24	1.41
12649--13045	14	28.2	14	72	17	114	2	12	56	29	1.47
12736--13046	27	11.7	25	72	17	138	2	12	56	28	1.48
12776--12827	23	2.3	22	90	3	77	3	9	51	34	1.53
12806--12873	15	4.6	15	76	10	77	5	5	48	39	1.52
12467--13046	20	27.9	20	76	12	218	3	9	56	30	1.47
12897--13117	7	31.0	7	77	13	96	0	13	69	16	1.24
12899--13046	81	1.8	79	90	8	237	0	14	62	22	1.31
12933--12990	9	7.2	9	77	18	58	0	13	65	20	1.26
13043--15564	1	2522.0	1	68	0	1372	10	1	83	4	0.84
13043--15566	7	361.1	7	81	12	2424	10	1	83	4	0.84
15614--18473	7	397.3	7	77	15	1460	39	45	9	6	1.61
16895--17239	20	16.3	20	72	22	126	41	51	2	5	1.37
16895--17165	120	2.4	107	78	16	275	41	52	0	5	1.31
17141--17199	23	2.6	23	83	5	75	47	49	0	3	1.18
16851--18829	7	280.6	7	76	12	756	38	49	6	6	1.53
21038--21063	12	2.2	12	100	0	52	19	7	23	50	1.73
32525--32550	13	2.0	13	100	0	52	30	15	15	38	1.88
32589--32664	21	3.7	21	82	3	109	28	18	11	40	1.86
32609--32682	20	3.7	20	81	3	103	31	20	13	35	1.91
32589--32682	41	2.3	41	100	0	188	29	19	12	38	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35133--35171	13	3.0	13	96	0	69	35	15	17	30	1.91
35157--35235	20	3.7	20	78	15	77	44	13	15	26	1.84
39075--39119	21	2.1	21	84	8	56	22	20	4	53	1.63
41333--41358	13	2.0	13	100	0	52	30	15	15	38	1.88
41397--41472	21	3.7	21	82	3	109	28	18	11	40	1.86
41417--41490	20	3.7	20	81	3	103	31	20	13	35	1.91
41397--41490	41	2.3	41	100	0	188	29	19	12	38	1.89
43635--43841	37	5.6	37	80	1	155	37	24	14	24	1.92
43678--43841	74	2.2	74	79	2	177	35	25	14	24	1.93
43636--43851	111	1.9	112	83	2	274	36	24	15	24	1.94
43995--44029	16	2.2	16	90	10	54	48	20	0	31	1.50
46480--46518	2	19.5	2	94	0	69	51	2	0	46	1.14
46518--46545	2	14.0	2	100	0	56	50	0	50	0	1.00
49444--49476	2	17.0	2	87	6	50	54	0	0	45	0.99
53699--53741	21	2.0	21	90	0	68	55	2	0	41	1.12
53707--53751	21	2.1	22	91	4	74	53	0	0	46	1.00
57976--58014	19	2.1	18	85	9	51	69	2	7	20	1.26
59142--59180	2	19.5	2	94	0	69	51	0	0	48	1.00
61082--61108	3	9.0	3	100	0	54	66	0	0	33	0.92
61146--61189	2	22.0	2	100	0	88	50	0	0	50	1.00
62942--63002	27	2.3	27	85	0	77	31	18	19	31	1.96
62952--63004	27	2.0	27	92	0	88	33	16	16	32	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
65759--65788	6	5.0	6	91	0	51	53	0	30	16	1.44
69953--69985	2	16.5	2	100	0	66	51	0	48	0	1.00
70722--70762	2	20.5	2	100	0	82	48	0	0	51	1.00
70796--70829	2	17.0	2	100	0	68	50	0	0	50	1.00
74296--74481	99	1.9	99	86	0	264	36	16	13	33	1.89
75322--75421	37	2.7	37	82	3	121	36	16	18	30	1.92
78490--78534	6	7.2	6	95	5	72	15	15	53	15	1.74
85206--85242	16	2.1	19	85	14	53	59	2	27	10	1.44
87089--87119	2	15.5	2	93	0	53	45	0	3	51	1.17
89734--89758	5	5.0	5	100	0	50	40	0	60	0	0.97
93948--93987	18	2.2	18	86	0	53	25	25	5	45	1.73
102982--103020	6	6.7	6	82	5	53	15	0	20	64	1.30
107795--107823	14	2.1	14	100	0	58	41	0	20	37	1.53
109167--109203	2	19.0	2	94	5	67	48	0	0	51	1.00
109729--109753	13	1.9	13	100	0	50	48	0	4	48	1.20
109818--109902	29	3.0	29	69	19	70	34	1	5	58	1.30
110906--110930	10	2.5	10	100	0	50	28	0	0	72	0.86
111143--111187	11	4.2	11	82	2	56	75	0	4	20	0.97
112329--112368	13	2.9	15	82	17	52	80	0	5	15	0.88
112330--112367	12	2.8	13	88	11	51	81	0	5	13	0.85
114439--114464	5	5.2	5	100	0	52	23	0	19	57	1.40
114926--114960	5	7.2	5	96	3	63	42	0	17	40	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
117325--117396	6	12.0	6	84	0	63	47	5	18	29	1.71
117339--117396	18	3.2	18	77	0	71	50	6	13	29	1.68
123003--123040	2	19.0	2	100	0	76	50	0	0	50	1.00
124071--124112	3	14.0	3	100	0	84	33	0	0	66	0.92
124523--124556	4	8.5	4	100	0	68	0	23	0	76	0.79
124703--124736	2	17.0	2	100	0	68	50	0	0	50	1.00
124774--124812	2	19.5	2	94	0	69	53	0	0	46	1.00
129789--129822	2	17.0	2	93	0	59	47	0	2	50	1.16
134602--134639	2	19.0	2	100	0	76	50	0	0	50	1.00
137839--137888	4	12.2	4	91	4	82	30	0	24	46	1.53
139373--139398	5	5.2	5	100	0	52	19	0	38	42	1.51
139419--139450	2	16.0	2	100	0	64	50	0	50	0	1.00
148642--148680	2	19.5	2	100	0	78	51	0	48	0	1.00
149346--149370	4	6.2	4	100	0	50	76	0	24	0	0.80
150783--150821	21	1.9	21	89	5	62	43	0	5	51	1.24
154039--154073	2	17.5	2	100	0	70	51	0	0	48	1.00
154982--155019	2	19.0	2	89	10	60	47	2	0	50	1.15
163204--163234	4	7.8	4	100	0	62	25	0	0	74	0.82
165988--166020	5	6.8	5	93	6	59	78	21	0	0	0.75
165988--166020	14	2.3	14	94	5	57	78	21	0	0	0.75
166244--166285	3	14.3	3	85	9	52	26	0	2	71	0.98
166594--166620	13	2.1	13	100	0	54	37	14	7	40	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
170057--170081	12	2.1	12	100	0	50	60	16	0	24	1.36
171204--171229	2	13.0	2	100	0	52	50	0	0	50	1.00
173272--173341	16	4.2	16	74	16	54	34	2	0	62	1.10
173282--173324	19	2.2	20	80	19	56	32	2	0	65	1.06
173909--173947	14	2.8	14	92	0	60	46	5	2	46	1.38
174456--174490	16	2.1	16	89	10	52	51	5	0	42	1.25
176950--177041	46	2.0	46	100	0	184	36	21	26	15	1.93
179138--179192	18	3.0	18	72	2	56	56	0	3	40	1.17
179264--179318	22	2.5	22	82	8	67	54	1	3	40	1.28
179282--179367	22	3.9	22	75	13	79	54	1	0	44	1.07
179282--179366	43	2.0	41	84	13	111	55	1	0	43	1.07
179341--179404	22	2.8	23	79	9	69	51	7	0	40	1.31
184259--184287	2	14.5	2	100	0	58	0	0	51	48	1.00
190253--190299	23	2.1	22	96	4	85	57	0	0	42	0.98
190565--190612	2	24.0	2	95	0	87	50	0	2	47	1.12
191648--191676	2	14.5	2	100	0	58	0	48	0	51	1.00
197423--197451	4	7.2	4	100	0	58	24	0	0	75	0.80
203010--203237	45	5.0	44	89	8	348	17	19	12	49	1.79
203010--203237	94	2.5	91	94	2	386	17	19	12	49	1.79
207789--207900	44	2.5	44	91	2	181	37	18	14	29	1.90
208007--208070	20	3.3	20	68	24	64	17	18	3	60	1.48
207985--208097	38	3.0	38	96	2	201	16	18	5	59	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
208027--208088	18	3.3	18	68	24	56	16	17	6	59	1.57
212529--212553	6	4.2	6	100	0	50	0	52	16	32	1.44
213181--213208	2	14.0	2	100	0	56	50	0	0	50	1.00
232169--232207	21	1.9	21	94	5	71	33	0	0	66	0.92
236265--236294	12	2.4	13	94	5	53	60	0	3	36	1.14
236840--236867	2	14.0	2	100	0	56	50	0	0	50	1.00
238429--238465	2	19.0	2	88	5	58	48	0	2	48	1.15
238584--238618	19	1.9	17	88	11	52	34	0	0	65	0.93
238597--238629	12	2.6	13	85	9	50	39	0	0	60	0.97
238603--238673	34	2.1	34	84	5	90	46	0	0	53	1.00

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16