genome.fa.s9405.2.7.7.80.10.50.1000.5.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: VEPZ01009405.1 Hibiscus syriacus cultivar Beakdansim tig00113337_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1310060

Tables:   1   2   3   4   5   6   

This is table  5  of  6  ( 657 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)
1005715--1005819	31	3.2	31	65	19	86	25	12	12	49	1.75
1010004--1010041	15	2.5	15	91	0	58	13	68	13	5	1.37
1018205--1018278	27	2.7	27	89	0	112	51	20	12	16	1.76
1018963--1019032	3	22.7	3	74	11	61	28	4	1	65	1.20
1018963--1019032	34	2.1	34	81	5	79	28	4	1	65	1.20
1020195--1020248	20	2.6	23	75	22	64	27	1	12	57	1.46
1024022--1024099	26	3.2	25	67	22	76	24	23	10	42	1.85
1024037--1024111	20	3.5	20	70	20	62	26	25	10	37	1.89
1024742--1024779	11	3.4	11	89	7	58	71	10	13	5	1.30
1025647--1025703	23	2.4	23	77	8	62	36	10	5	47	1.61
1026563--1026801	105	2.3	102	82	6	268	30	19	11	37	1.88
1026763--1026866	36	3.0	36	80	6	117	32	20	11	35	1.88
1027112--1027171	28	2.1	28	90	6	95	33	8	13	45	1.73
1027079--1027344	143	1.9	142	88	6	412	32	11	14	41	1.81
1027253--1027387	30	4.3	30	76	10	137	35	9	13	41	1.77
1027276--1027441	65	2.5	67	94	2	284	30	11	11	46	1.75
1027270--1027483	65	3.3	65	86	5	247	30	11	12	45	1.78
1028407--1028483	28	2.6	28	82	17	95	25	15	11	46	1.80
1028433--1028503	28	2.5	28	84	4	90	25	14	12	47	1.79
1028910--1028979	3	22.7	3	77	11	70	30	4	1	64	1.21
1028904--1028981	28	2.7	28	82	9	77	28	3	1	66	1.17
1028910--1028979	34	2.1	34	83	5	88	30	4	1	64	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1030124--1030172	19	2.5	21	83	12	68	24	2	14	59	1.46
1030122--1030170	20	2.4	22	80	16	68	26	2	14	57	1.48
1036414--1036462	21	2.4	21	79	3	55	46	6	6	40	1.53
1041351--1041383	1	33.0	1	100	0	66	0	0	0	100	0.00
1046863--1046899	2	18.5	2	100	0	74	48	0	0	51	1.00
1047757--1047912	21	7.7	21	78	9	112	33	23	19	23	1.97
1047842--1047893	20	2.6	20	96	0	95	28	21	21	28	1.98
1048267--1048326	31	1.9	31	86	0	84	28	8	8	55	1.59
1048877--1049012	54	2.5	53	89	3	193	33	22	15	27	1.95
1048991--1049147	55	2.9	54	79	3	163	31	12	21	34	1.91
1049382--1049562	46	3.9	46	91	0	263	46	9	18	24	1.80
1049481--1049553	22	3.2	22	65	14	58	42	12	23	21	1.87
1050300--1050370	23	3.2	23	78	5	76	53	14	18	14	1.73
1054177--1054282	48	2.2	48	96	1	196	33	26	19	20	1.97
1061619--1061666	23	2.1	23	84	0	60	37	6	16	39	1.74
1061895--1061933	20	2.0	20	89	0	60	35	15	7	41	1.76
1062285--1062740	182	2.5	182	89	0	680	28	14	12	44	1.81
1062611--1062961	111	3.1	111	92	2	578	26	13	12	46	1.80
1072378--1072653	138	2.0	138	99	0	543	38	16	17	27	1.91
1079340--1079395	2	28.0	2	100	0	112	50	0	0	50	1.00
1080869--1080894	2	13.0	2	100	0	52	50	0	0	50	1.00
1083166--1083202	18	2.2	16	90	9	56	40	0	0	59	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1083259--1083363	55	1.9	54	83	12	135	42	2	3	50	1.35
1083443--1083513	24	3.0	22	80	15	63	53	1	2	42	1.24
1085628--1085657	7	4.4	7	95	4	53	73	0	0	26	0.84
1085623--1085672	23	2.1	24	85	7	66	72	0	4	24	1.02
1085953--1085987	2	18.0	2	94	5	63	48	0	0	51	1.00
1087161--1087213	19	2.8	19	100	0	106	47	11	5	35	1.63
1088816--1088879	23	2.8	23	90	0	101	26	26	28	18	1.98
1088890--1089112	103	2.2	103	97	0	419	36	23	13	26	1.91
1089864--1090088	64	3.5	64	82	7	244	28	19	19	32	1.96
1091788--1091838	19	2.7	18	77	14	50	39	0	1	58	1.09
1092290--1092324	2	17.5	2	100	0	70	51	0	0	48	1.00
1101028--1101108	25	3.4	23	75	11	74	43	3	1	51	1.27
1101521--1101586	21	3.2	21	70	18	66	22	24	19	33	1.97
1101479--1101610	41	3.2	41	90	1	201	22	21	23	32	1.98
1102385--1102422	6	6.5	6	96	3	69	0	15	52	31	1.43
1102502--1102570	21	3.3	20	69	16	61	34	23	21	20	1.96
1102500--1102715	41	5.2	41	84	3	279	32	24	19	23	1.97
1102500--1102715	84	2.6	83	88	2	326	32	24	19	23	1.97
1102607--1102715	21	5.2	20	64	22	55	33	25	18	22	1.97
1103713--1103737	2	12.5	2	100	0	50	48	0	0	52	1.00
1104085--1104660	113	5.1	112	91	0	902	46	13	14	25	1.82
1104530--1104986	182	2.5	182	87	3	659	44	12	15	27	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1105411--1105467	23	2.4	23	76	2	69	36	14	12	36	1.83
1105615--1105674	23	2.6	23	83	0	75	41	8	13	36	1.74
1105525--1105758	87	2.7	87	91	1	380	43	10	12	33	1.78
1105702--1105784	23	3.6	23	88	0	112	42	8	16	32	1.79
1105615--1105871	110	2.3	110	89	1	390	43	10	12	33	1.78
1105734--1105964	87	2.7	86	89	2	356	44	11	12	32	1.78
1105812--1105871	23	2.6	23	83	0	66	45	10	11	33	1.74
1105544--1105956	197	2.1	196	93	0	693	43	10	12	32	1.77
1105899--1105946	23	2.2	21	85	7	60	39	10	16	33	1.83
1106503--1106941	198	2.2	197	86	4	616	29	14	14	41	1.85
1107146--1107186	21	2.0	22	85	9	59	53	2	0	43	1.13
1110559--1110614	22	2.4	23	82	8	69	30	23	17	28	1.97
1117033--1117080	24	2.1	22	84	7	60	45	0	0	54	0.99
1126927--1126954	2	14.0	2	100	0	56	50	0	0	50	1.00
1127678--1127709	6	5.3	6	100	0	64	15	15	34	34	1.90
1129453--1129549	31	3.2	31	64	19	85	34	13	6	46	1.68
1129452--1129573	61	2.0	61	100	0	244	32	14	6	45	1.71
1130692--1130731	22	2.0	20	85	14	55	27	7	5	60	1.45
1131165--1131194	14	2.1	14	93	0	51	53	3	0	43	1.17
1133994--1134061	31	2.2	31	97	0	127	13	29	30	26	1.94
1134392--1134428	6	6.2	6	100	0	74	35	48	16	0	1.46
1135057--1135105	22	2.2	22	96	0	89	38	28	16	16	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1135417--1135477	2	30.5	2	100	0	122	50	0	0	49	1.00
1136264--1136300	18	2.1	18	89	0	56	51	10	0	37	1.37
1136827--1136873	6	7.8	6	97	0	85	53	17	29	0	1.44
1139314--1139430	56	2.1	56	90	3	182	29	5	6	58	1.46
1148086--1148128	19	2.3	19	100	0	86	32	13	23	30	1.93
1148338--1148396	14	4.1	14	78	4	64	40	6	16	35	1.76
1148340--1148398	29	2.0	29	96	0	109	42	8	16	32	1.79
1148621--1148690	31	2.2	29	77	20	70	47	0	4	48	1.21
1148721--1148771	23	2.2	23	82	0	57	43	1	3	50	1.31
1148759--1148827	19	3.6	19	71	21	63	47	0	2	49	1.16
1148953--1149014	22	2.9	21	83	11	72	56	0	0	43	0.99
1148952--1148997	10	4.5	10	78	21	51	58	0	0	41	0.98
1149216--1149309	42	2.2	42	90	0	143	47	17	17	18	1.82
1152373--1152424	25	2.1	25	92	0	86	15	15	26	42	1.87
1153947--1153989	14	3.1	14	82	0	50	30	16	6	46	1.73
1154791--1154826	18	2.0	18	94	0	63	41	5	22	30	1.76
1154809--1155077	89	2.9	94	84	7	359	41	11	18	28	1.86
1157133--1157158	13	2.0	13	100	0	52	46	0	15	38	1.46
1158780--1158853	21	3.3	21	81	17	94	29	4	2	63	1.26
1158773--1158846	26	3.0	25	81	18	102	32	4	1	62	1.22
1158775--1158858	26	3.5	24	75	25	88	28	3	2	65	1.22
1158937--1158980	19	2.3	20	80	11	56	63	0	0	36	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1163059--1163093	2	17.5	2	100	0	70	51	0	0	48	1.00
1167379--1167442	3	21.3	3	100	0	128	32	0	0	67	0.91
1170125--1170160	13	3.0	12	88	11	56	58	0	0	41	0.98
1171286--1171388	36	2.9	36	82	2	118	41	20	17	20	1.90
1171388--1171412	2	12.5	2	100	0	50	52	0	0	48	1.00
1174151--1174187	7	5.4	7	93	6	67	24	29	29	16	1.96
1174151--1174187	13	2.7	14	91	8	67	24	29	29	16	1.96
1174177--1174234	17	3.4	17	92	0	98	17	22	41	18	1.90
1181441--1181498	17	3.4	17	87	0	89	17	22	39	20	1.92
1181494--1181563	19	3.7	19	82	5	70	27	28	22	21	1.99

Tables:   1   2   3   4   5   6