genome.fa.s1700.2.7.7.80.10.50.1000.5.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  5  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)
904859--904931	17	4.2	17	74	22	62	9	12	0	78	0.98
939176--939220	23	2.0	22	82	4	54	20	28	8	42	1.82
941297--941363	27	2.5	27	80	0	80	46	20	7	25	1.77
945803--945925	39	3.2	39	83	4	142	47	20	4	28	1.68
957679--957710	2	16.0	2	100	0	64	50	0	0	50	1.00
958355--958407	20	2.7	20	100	0	106	20	28	32	18	1.97
960472--960559	32	2.8	32	78	3	97	20	29	25	25	1.99
960472--960580	32	3.4	30	73	12	76	20	27	23	28	1.99
961041--961103	31	2.0	31	81	9	74	31	4	4	58	1.39
966481--966522	21	2.0	21	86	9	59	35	16	9	38	1.81
967831--967897	24	2.8	24	80	8	64	77	1	11	8	1.05
969850--970015	58	2.9	57	86	6	219	32	8	18	40	1.80
970271--970359	38	2.3	38	80	0	115	32	16	13	37	1.88
970375--970497	59	2.1	59	84	0	156	26	28	17	27	1.98
970515--970612	39	2.5	39	83	3	108	33	11	14	40	1.81
970247--970828	252	2.3	252	85	3	798	30	21	15	31	1.95
970767--971019	39	6.5	39	83	3	303	30	16	16	35	1.91
970767--971019	79	3.2	78	82	3	312	30	16	16	35	1.91
971768--971808	2	20.5	2	94	0	73	48	2	0	48	1.14
972594--972634	22	1.9	22	85	14	59	24	14	7	53	1.66
976347--976408	2	31.0	2	100	0	124	50	0	0	50	1.00
979094--979197	41	2.5	41	82	13	124	34	17	20	27	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
979162--979239	40	1.9	42	84	5	106	39	15	17	26	1.90
980263--980449	57	3.3	57	99	0	367	29	5	13	50	1.65
980647--980732	42	2.0	41	82	8	102	34	8	19	37	1.82
980711--980805	41	2.3	41	90	3	156	23	18	23	34	1.96
980711--980820	41	2.7	41	81	16	138	23	20	23	31	1.98
980793--980909	42	2.8	42	80	11	118	29	17	23	29	1.97
980841--980949	42	2.6	42	81	10	107	31	18	19	31	1.96
981731--981821	46	2.0	46	95	0	164	12	24	14	49	1.77
983376--983523	43	3.4	43	88	0	197	33	26	17	22	1.96
983376--983566	43	4.4	43	86	2	177	32	26	18	21	1.97
983370--983695	86	3.8	86	78	4	237	30	26	17	25	1.98
983462--983695	43	5.4	43	86	1	263	27	26	18	27	1.98
987286--987405	32	3.8	32	76	8	111	20	25	25	28	1.99
988900--988980	30	2.9	29	70	17	80	38	2	1	58	1.20
989296--989329	2	17.0	2	100	0	68	50	0	0	50	1.00
998246--998287	18	2.3	18	95	0	75	52	11	4	30	1.59
998374--998398	7	3.6	7	100	0	50	40	0	12	48	1.40
999791--999846	9	6.2	9	77	8	51	41	0	0	58	0.98
999812--999846	3	12.0	3	87	6	54	34	0	0	65	0.93
999795--999840	20	2.3	20	85	3	58	41	0	0	58	0.98
1000621--1000651	16	1.9	16	93	0	53	77	0	22	0	0.77
1000659--1000724	28	2.4	28	97	0	123	33	0	45	21	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1007848--1007877	13	2.3	13	100	0	60	16	46	23	13	1.82
1008073--1008105	17	2.0	17	88	5	50	39	18	9	33	1.82
1010363--1010453	24	3.8	24	83	2	112	26	17	18	37	1.93
1010363--1010453	47	1.9	48	86	2	130	26	17	18	37	1.93
1010530--1010604	35	2.1	35	97	0	141	9	29	28	33	1.88
1012332--1012399	33	2.1	33	83	5	84	20	5	13	60	1.54
1018559--1019126	38	14.2	38	75	11	406	26	16	16	39	1.90
1018559--1019080	80	6.6	76	77	9	388	26	16	16	39	1.90
1018567--1019211	38	15.9	40	73	11	314	26	16	17	39	1.90
1018803--1019163	80	4.3	87	75	11	229	26	17	16	38	1.91
1018803--1019159	167	2.1	165	79	5	387	26	17	16	38	1.91
1019912--1020433	134	3.9	133	84	1	668	29	17	18	34	1.94
1022570--1022684	47	2.6	45	86	6	162	41	8	19	30	1.81
1030308--1030334	13	2.1	13	100	0	54	29	0	0	70	0.88
1035248--1035307	3	20.3	3	93	3	104	70	0	0	30	0.88
1049208--1049251	17	2.6	17	85	3	63	31	2	0	65	1.05
1052388--1052437	2	25.0	2	100	0	100	50	0	0	50	1.00
1052987--1053055	14	4.7	15	72	19	56	14	18	49	17	1.80
1053013--1053060	18	2.6	18	90	3	69	12	18	50	18	1.78
1053048--1053112	24	2.7	25	78	7	62	16	26	41	15	1.88
1069838--1069957	48	2.6	45	80	7	141	40	7	21	30	1.81
1075482--1075581	16	5.8	16	67	19	51	73	0	22	5	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1075476--1075551	31	2.5	30	75	14	75	72	0	22	5	1.04
1075479--1075564	40	2.2	40	79	8	95	72	0	23	4	1.04
1075495--1075584	47	1.9	47	82	8	112	71	0	22	6	1.09
1076877--1077623	38	18.5	40	75	10	464	26	17	16	39	1.91
1076877--1077488	80	7.7	76	77	9	365	26	16	16	39	1.91
1077234--1077535	80	3.8	79	74	10	254	29	16	15	38	1.90
1077541--1077668	44	2.9	44	75	9	116	23	18	18	39	1.93
1077507--1077681	45	3.9	45	77	5	158	25	17	18	38	1.93
1078321--1078900	134	4.3	134	82	5	665	30	17	17	34	1.93
1079684--1079741	2	29.0	2	100	0	116	50	0	0	50	1.00
1081283--1081312	2	15.0	2	100	0	60	50	0	0	50	1.00
1081608--1081641	13	2.9	11	84	16	50	44	0	0	55	0.99
1081610--1081637	13	2.2	13	100	0	56	35	0	0	64	0.94
1085192--1085225	2	17.0	2	100	0	68	50	0	0	50	1.00
1086830--1086875	24	1.9	24	86	8	67	23	17	6	52	1.68
1087045--1087081	2	18.5	2	100	0	74	48	0	0	51	1.00
1090649--1090729	41	2.0	41	92	0	135	45	17	14	22	1.84
1091501--1091644	70	2.1	70	95	0	261	38	19	2	39	1.66
1097668--1097694	2	13.5	2	100	0	54	48	0	0	51	1.00
1101167--1101222	26	2.2	25	80	3	67	78	0	16	5	0.92
1102486--1102862	136	2.8	132	83	5	441	31	19	19	29	1.96
1106871--1107197	80	4.1	80	86	2	424	31	25	21	21	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1110252--1110299	22	2.1	23	88	11	73	50	25	0	25	1.50
1112226--1112553	80	4.1	80	87	1	460	30	25	21	22	1.99
1116414--1116482	35	2.0	35	91	0	111	30	0	26	43	1.55
1119975--1120009	17	2.1	17	100	0	70	34	17	31	17	1.93
1126823--1126906	31	2.7	31	77	5	80	28	32	26	13	1.93
1151757--1151834	39	2.0	38	87	2	111	26	19	19	34	1.95
1152508--1152557	25	2.1	25	85	14	70	30	0	6	64	1.18
1152870--1152967	51	1.9	51	87	0	142	41	10	6	41	1.63
1161564--1161630	30	2.2	30	94	0	116	37	2	14	44	1.61
1161894--1161988	30	3.2	30	90	0	154	36	4	14	44	1.65
1166939--1166991	21	2.5	21	81	6	72	20	26	18	33	1.96
1166981--1167032	21	2.5	21	87	3	70	38	17	23	21	1.93
1167018--1167095	41	1.9	41	86	0	111	37	24	17	20	1.94
1167063--1167155	20	4.7	20	89	0	123	26	25	20	26	1.99
1167021--1167155	40	3.3	40	81	3	137	31	25	19	23	1.98
1167309--1167342	12	2.9	12	86	4	52	17	41	5	35	1.74
1167897--1167950	24	2.2	24	90	0	81	22	16	20	40	1.91
1168125--1168149	12	2.1	12	100	0	50	72	0	28	0	0.86
1170485--1170568	19	4.7	19	87	10	124	14	20	17	47	1.82
1170485--1170581	38	2.8	33	82	14	131	13	21	18	46	1.83
1170708--1170744	14	2.6	14	86	0	56	48	21	0	29	1.50
1172154--1172245	42	2.2	42	88	1	141	20	15	42	21	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1172181--1172241	21	2.9	21	73	9	70	21	13	42	22	1.87
1172590--1172714	20	6.7	19	72	11	80	44	23	18	13	1.85
1172678--1172725	19	2.5	19	86	6	71	47	27	16	8	1.75
1172721--1172803	19	4.6	19	79	14	113	13	20	20	45	1.84
1172788--1172842	20	2.8	19	83	8	65	16	23	23	36	1.94
1173130--1173172	20	2.2	20	91	0	68	37	25	20	16	1.93
1173130--1173215	19	4.4	20	82	1	77	41	20	20	16	1.90
1173241--1173312	19	3.8	19	96	0	126	12	20	19	47	1.82
1173327--1173381	20	2.8	19	83	8	65	16	23	23	36	1.94
1173916--1173963	18	2.7	18	93	0	87	14	12	45	27	1.81

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