genome.fa.s1700.2.7.7.80.10.50.1000.6.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: VEPZ01001700.1 Hibiscus syriacus cultivar Beakdansim tig00003398_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2632955

Tables:   1   2   3   4   5   6   7   8   9   10   11   

This is table  6  of  11  ( 1314 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)
1175290--1175348	20	3.0	20	87	0	73	42	22	18	16	1.89
1175620--1175662	22	2.0	22	95	0	77	20	16	41	20	1.90
1175849--1176003	20	7.7	20	80	8	161	22	18	26	32	1.97
1175829--1176003	61	2.9	61	78	10	203	22	17	25	33	1.96
1175829--1176004	20	8.7	19	79	9	136	22	17	25	34	1.96
1175829--1176007	41	4.4	41	88	4	254	22	17	25	35	1.95
1175988--1176047	20	2.9	21	77	7	59	23	23	15	38	1.92
1176034--1176086	21	2.5	22	75	6	65	35	18	24	20	1.95
1177051--1177168	15	7.5	15	81	13	139	45	0	2	51	1.14
1177148--1177791	32	17.4	33	68	24	266	34	0	13	52	1.43
1177171--1177213	22	2.0	22	95	0	77	34	0	11	53	1.37
1177066--1177248	69	2.7	67	77	9	208	42	0	6	51	1.28
1177148--1177819	54	12.3	54	73	17	412	34	0	12	52	1.42
1177225--1177267	22	2.0	22	95	0	77	37	0	11	51	1.39
1177247--1177396	80	1.9	80	95	0	273	32	0	15	52	1.43
1177148--1177759	188	3.2	188	92	4	977	33	0	13	52	1.43
1177413--1177455	22	2.0	22	95	0	77	37	0	11	51	1.39
1177458--1177505	22	2.4	18	73	23	51	33	0	14	52	1.42
1177489--1177610	26	4.6	25	69	20	79	28	1	16	53	1.53
1177435--1177647	80	2.7	80	98	0	408	32	0	14	52	1.48
1177538--1177585	22	2.4	18	73	23	51	33	0	14	52	1.42
1177604--1177656	14	3.5	14	72	18	52	37	0	5	56	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1177514--1177808	112	2.6	112	96	0	554	32	0	13	53	1.43
1177618--1177674	18	3.4	17	72	18	57	35	0	10	54	1.35
1177771--1177813	22	2.0	22	100	0	86	34	0	13	51	1.42
1177837--1177896	31	1.9	31	93	0	102	43	10	6	40	1.64
1178969--1179058	32	2.9	31	73	12	94	27	33	23	15	1.95
1179931--1180114	29	6.4	28	96	2	323	46	17	3	32	1.64
1179931--1180114	57	3.2	57	96	2	334	46	17	3	32	1.64
1179959--1180300	58	5.9	56	87	3	233	46	15	5	31	1.69
1179960--1180144	86	2.2	86	88	2	255	47	17	4	29	1.69
1180815--1180920	53	2.0	53	83	7	135	32	18	7	41	1.79
1182764--1182820	25	2.3	24	80	14	62	38	19	5	36	1.74
1185384--1185434	22	2.3	23	89	3	77	15	23	43	17	1.88
1185972--1186000	9	3.2	9	100	0	58	68	0	31	0	0.89
1187570--1187638	12	5.8	12	77	6	68	53	18	13	14	1.72
1187568--1187638	24	3.0	24	77	6	90	53	18	12	15	1.73
1187569--1187676	24	4.5	24	71	9	87	49	17	14	18	1.80
1187568--1187659	48	1.9	48	86	8	134	50	17	14	18	1.79
1192306--1192374	12	5.8	12	76	6	59	53	17	13	15	1.73
1192304--1192374	24	3.0	24	75	6	81	53	16	12	16	1.73
1198520--1198585	24	2.8	24	80	0	87	56	18	7	18	1.64
1200958--1200990	16	2.0	17	88	5	50	27	36	21	15	1.93
1203147--1203181	15	2.3	15	95	0	61	28	31	22	17	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1211584--1211641	19	2.9	21	84	7	75	43	18	17	20	1.89
1211655--1211769	57	2.0	57	100	0	230	39	22	17	20	1.93
1211725--1211839	20	5.6	20	77	12	117	35	27	17	19	1.94
1211724--1211842	41	2.9	42	87	5	154	36	26	16	19	1.93
1213874--1214065	93	2.1	92	91	2	305	23	11	17	46	1.81
1213998--1214123	63	2.0	63	92	3	209	21	11	17	50	1.77
1214175--1214308	19	7.4	19	70	19	99	47	21	19	11	1.81
1214233--1214288	14	3.6	14	76	21	58	46	21	21	10	1.81
1214214--1214327	33	3.5	33	91	0	183	48	21	20	9	1.78
1214655--1214748	42	2.2	42	79	7	102	24	34	19	22	1.97
1215969--1216145	83	2.1	83	95	2	320	37	2	18	41	1.63
1216113--1216148	14	2.6	14	95	0	63	33	0	22	44	1.53
1216285--1216835	33	16.2	33	87	8	775	13	22	19	44	1.86
1216298--1216802	19	29.4	19	70	21	352	13	22	19	44	1.85
1216285--1216835	105	5.4	99	91	5	775	13	22	19	44	1.86
1216485--1216605	14	7.6	14	68	24	71	11	23	19	46	1.82
1216296--1216801	171	2.9	171	94	2	856	13	22	19	44	1.86
1216656--1216710	14	3.6	14	73	21	56	10	23	20	45	1.82
1216760--1216787	14	2.0	14	100	0	56	14	21	21	42	1.88
1219303--1219356	24	2.2	24	93	0	90	40	20	18	20	1.91
1219303--1219370	24	2.8	24	84	0	64	38	20	17	23	1.93
1219482--1219515	12	2.8	12	90	0	50	14	0	29	55	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1220177--1220488	20	15.4	20	75	11	242	19	17	23	39	1.92
1220177--1220427	41	6.2	41	87	4	275	19	17	24	38	1.93
1225284--1225315	2	16.0	2	100	0	64	50	0	0	50	1.00
1225284--1225338	10	5.6	10	83	10	51	52	0	3	43	1.18
1225536--1225562	2	13.5	2	100	0	54	51	0	0	48	1.00
1232078--1232195	33	3.6	33	83	4	159	31	12	22	33	1.92
1232078--1232213	65	2.1	65	84	5	177	30	13	22	33	1.92
1232324--1232409	34	2.5	34	84	3	111	34	19	10	34	1.86
1232628--1232723	40	2.4	40	91	0	156	29	13	11	45	1.78
1232731--1232968	36	6.5	36	86	3	280	26	21	13	39	1.90
1232992--1233111	61	2.0	61	86	8	172	32	19	11	36	1.88
1233351--1233933	136	4.3	136	94	1	956	32	19	22	25	1.97
1233997--1234139	76	1.9	76	89	2	225	41	16	20	21	1.89
1234071--1234269	91	2.2	91	88	4	303	37	17	20	24	1.93
1236074--1236109	2	18.0	2	100	0	72	50	0	0	50	1.00
1241587--1241620	2	17.0	2	87	0	50	44	0	5	50	1.26
1241802--1241849	15	3.4	14	82	11	62	85	2	12	0	0.69
1241803--1241849	7	6.7	7	80	9	60	85	2	12	0	0.70
1242878--1242995	33	3.6	33	83	4	159	31	12	22	33	1.92
1242878--1243013	65	2.1	65	84	5	177	30	13	22	33	1.92
1243124--1243203	34	2.4	33	85	4	106	36	21	10	32	1.86
1243379--1243525	80	1.9	80	81	7	183	28	13	13	44	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1243430--1243525	40	2.4	40	91	0	156	29	13	11	45	1.78
1243533--1243770	36	6.5	36	86	3	280	26	21	13	39	1.90
1243794--1243914	62	2.0	62	85	9	167	33	19	11	36	1.87
1244154--1244732	136	4.3	136	95	0	982	32	19	22	25	1.98
1244819--1244883	20	3.3	20	67	18	55	44	12	21	21	1.85
1244800--1245086	91	3.2	92	87	5	413	39	15	20	24	1.92
1251522--1251546	2	12.5	2	100	0	50	48	0	0	52	1.00
1251544--1251572	12	2.3	13	94	5	51	34	13	0	51	1.42
1255214--1255251	19	2.1	19	90	9	62	15	7	5	71	1.28
1262163--1262205	7	6.0	7	86	13	61	81	0	16	2	0.79
1262163--1262205	13	3.0	14	86	13	61	81	0	16	2	0.79
1262244--1262314	6	11.8	6	78	13	67	81	1	16	0	0.76
1262243--1262308	8	8.5	8	75	11	66	81	1	16	0	0.76
1262243--1262314	24	3.1	24	84	11	105	81	1	16	0	0.75
1262243--1262314	30	2.6	29	79	20	75	81	1	16	0	0.75
1262130--1262284	79	2.0	79	84	5	206	58	9	21	9	1.58
1265435--1265465	3	10.3	3	100	0	62	32	0	0	67	0.91
1266306--1266345	21	1.9	21	85	10	55	35	27	20	17	1.95
1277255--1277315	17	3.4	17	73	10	59	55	1	6	36	1.36
1277975--1278083	55	2.0	55	96	0	200	32	5	25	36	1.79
1279710--1279756	15	3.1	15	81	6	51	57	2	0	40	1.11
1282602--1282714	39	2.9	40	85	4	133	42	24	4	28	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1282622--1282714	39	2.4	39	90	1	150	43	23	5	27	1.76
1283875--1283916	17	2.7	16	79	13	52	21	4	7	66	1.35
1285643--1285685	22	2.0	22	90	0	68	20	16	34	27	1.94
1285672--1285754	22	3.9	21	75	10	69	19	24	28	27	1.98
1286630--1286685	26	2.2	26	83	6	69	39	23	14	23	1.91
1287715--1287792	32	2.4	32	89	4	113	16	23	30	29	1.96
1288743--1288935	98	2.0	97	88	3	289	34	16	17	32	1.92
1290352--1290398	2	23.5	2	100	0	94	48	0	0	51	1.00
1291290--1291344	21	2.9	19	81	10	60	16	3	5	74	1.15
1299044--1299087	2	22.0	2	100	0	88	50	0	0	50	1.00

Tables:   1   2   3   4   5   6   7   8   9   10   11