genome.fa.s8855.2.7.7.80.10.50.1000.4.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: VEPZ01008855.1 Hibiscus syriacus cultivar Beakdansim tig00112072_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1316246

Tables:   1   2   3   4   5   

This is table  4  of  5  ( 571 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)
858655--858810	70	2.2	69	78	1	177	23	15	18	42	1.88
858957--859024	13	5.2	13	87	0	91	27	19	17	35	1.94
858950--859004	26	2.1	26	82	0	65	32	18	16	32	1.93
859181--859218	2	19.5	2	94	5	69	47	0	0	52	1.00
861933--861967	18	1.9	18	88	0	52	77	2	17	2	1.02
864199--864230	2	16.0	2	100	0	64	50	0	0	50	1.00
866909--866947	14	2.8	13	88	3	51	61	10	12	15	1.56
867041--867079	17	2.4	16	84	16	53	43	0	12	43	1.42
868288--868366	36	2.3	35	82	4	97	31	11	10	46	1.73
868306--868377	36	2.0	35	81	10	83	27	11	12	48	1.75
873338--873375	18	2.1	19	90	5	60	63	0	13	23	1.30
877562--877622	18	3.3	18	88	6	79	3	21	1	73	1.06
877577--877622	19	2.5	18	92	3	74	4	21	2	71	1.14
882094--882120	11	2.5	11	100	0	54	33	14	18	33	1.92
897870--897931	32	1.9	32	93	6	108	29	20	14	35	1.93
903029--903088	29	2.1	29	90	6	95	33	13	25	28	1.93
911306--911332	2	13.5	2	100	0	54	48	0	0	51	1.00
912545--912571	13	2.1	13	100	0	54	55	0	7	37	1.28
924370--924405	11	3.2	11	92	4	54	38	0	16	44	1.48
932293--932324	16	1.9	17	93	6	57	81	6	6	6	0.99
934365--934423	17	3.5	17	68	13	50	30	13	8	47	1.73
934414--934459	18	2.6	18	92	0	74	32	6	13	47	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
936244--936292	17	2.9	17	81	0	62	42	16	4	36	1.67
936692--936746	25	2.2	25	96	0	101	32	21	20	25	1.97
937965--938007	17	2.5	17	100	0	86	13	23	9	53	1.69
939673--939721	17	2.9	17	81	0	62	42	16	4	36	1.67
940123--940171	25	2.0	25	95	0	89	36	22	14	26	1.92
947175--947260	34	2.5	34	84	1	109	30	10	26	32	1.90
948286--948314	2	14.5	2	100	0	58	48	0	0	51	1.00
948420--948454	3	12.0	3	93	6	63	31	0	0	68	0.90
951464--951522	23	2.6	23	80	0	73	40	1	13	44	1.54
951535--951757	76	3.0	75	82	8	260	47	3	6	43	1.45
951534--951757	36	6.1	36	86	5	279	46	3	6	43	1.45
951811--951881	3	21.7	3	78	21	56	30	1	0	67	0.99
951810--951873	13	4.9	13	76	16	62	31	1	0	67	1.00
951811--951880	20	3.5	20	81	9	90	31	1	0	67	1.00
951792--951881	10	9.0	10	76	18	71	32	1	2	64	1.13
951810--951881	7	10.3	7	74	16	69	30	1	0	68	0.99
953231--953258	6	4.7	6	100	0	56	14	14	0	71	1.15
954490--954528	20	2.0	20	85	10	53	51	15	5	28	1.64
962331--963068	369	2.0	375	94	3	1316	34	16	21	27	1.94
965008--965067	23	2.5	24	83	2	86	40	1	11	46	1.50
965032--965322	37	7.9	35	79	12	284	43	4	8	43	1.55
965032--965322	73	4.0	71	78	12	302	43	4	8	43	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
965201--965361	76	2.1	76	82	3	191	46	4	8	40	1.55
965414--965489	13	6.5	12	75	23	65	31	1	1	65	1.09
965414--965490	3	25.3	3	75	23	56	31	1	1	66	1.08
965416--965492	22	3.5	22	73	18	72	29	1	1	67	1.07
966636--966670	13	2.6	13	90	4	52	11	8	0	80	0.92
969364--969437	37	2.0	37	94	0	130	35	10	18	35	1.86
969974--970010	2	18.5	2	100	0	74	48	0	0	51	1.00
970572--970661	44	2.0	45	97	2	173	45	4	6	43	1.50
970641--970666	2	13.0	2	100	0	52	50	0	0	50	1.00
971058--971104	2	24.0	2	95	4	87	48	0	0	51	1.00
971408--971446	14	2.9	13	81	7	51	58	5	0	35	1.20
973859--973891	14	2.4	14	90	5	50	63	3	6	27	1.32
975428--976029	104	5.8	105	82	6	692	23	19	17	39	1.92
976912--977001	9	9.4	9	74	17	67	6	13	1	78	0.99
980790--980833	21	2.1	21	100	0	88	13	29	4	52	1.60
988927--988957	15	2.0	16	93	6	55	58	3	6	32	1.40
994389--994542	42	3.7	41	73	11	134	31	20	16	32	1.94
994438--994854	83	5.0	83	75	9	310	35	16	17	31	1.92
996437--996473	18	2.0	19	89	5	58	40	10	2	45	1.53
999169--999415	81	3.1	79	84	6	289	31	22	10	35	1.88
999816--1000015	95	2.1	95	85	3	285	23	24	14	38	1.92
1006112--1006361	81	3.1	81	88	2	349	32	23	10	34	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1006768--1006954	95	2.0	95	82	2	232	26	25	8	39	1.85
1008099--1008145	22	2.1	22	88	0	67	25	6	0	68	1.13
1008096--1008143	3	15.7	3	82	4	60	25	6	0	68	1.12
1008172--1008254	23	3.6	23	77	9	89	44	40	9	4	1.58
1025180--1025439	141	1.9	140	85	4	362	37	14	20	27	1.92
1025752--1025821	23	3.0	23	82	2	86	45	41	8	4	1.54
1033803--1033979	90	2.0	89	92	1	291	37	11	6	44	1.68
1037573--1037665	46	2.0	46	97	0	177	21	7	17	53	1.68
1037584--1037656	23	3.2	23	62	27	55	19	8	16	56	1.65
1038746--1038780	15	2.3	15	100	0	70	28	20	28	22	1.98
1038925--1038977	23	2.4	22	84	9	72	52	9	9	28	1.64
1040717--1040786	22	3.3	21	70	16	63	50	2	4	42	1.37
1042686--1042721	16	2.2	17	90	5	56	66	2	5	25	1.27
1067369--1067427	31	1.9	31	83	10	77	45	10	20	23	1.81
1067379--1067443	29	2.2	31	83	10	82	43	10	21	24	1.84
1072363--1072392	13	2.2	14	94	5	53	20	26	13	40	1.89
1082883--1082943	21	2.8	21	70	5	50	63	8	0	27	1.22
1082943--1082971	2	15.0	2	92	7	51	51	0	0	48	1.00
1083306--1083352	23	1.9	23	83	12	58	53	4	2	40	1.32
1083612--1083665	24	2.3	22	77	20	56	37	0	5	57	1.22
1085415--1085471	20	2.5	24	86	13	70	43	0	1	54	1.10
1085423--1085471	20	2.3	23	89	10	77	44	0	0	55	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1085422--1085488	23	2.9	22	79	12	80	43	1	0	55	1.09
1088068--1088112	3	15.3	3	78	21	51	64	0	0	35	0.94
1088268--1090369	54	39.2	54	85	2	2655	21	25	19	33	1.97
1088268--1090369	269	7.9	269	85	1	2628	21	25	19	33	1.97
1090742--1090822	42	1.9	42	89	0	126	32	20	22	24	1.98
1090830--1090948	37	3.2	37	89	0	193	22	18	21	36	1.95
1092202--1092327	7	17.9	7	88	4	173	0	11	0	87	0.59
1092215--1092326	1	112.0	1	78	0	116	0	10	0	89	0.49
1092377--1092558	1	182.0	1	87	0	184	2	6	1	89	0.65
1095345--1095390	19	2.4	19	100	0	92	17	28	19	34	1.94
1103907--1103945	18	2.2	18	85	0	51	58	2	2	35	1.25
1106100--1106135	3	11.3	3	88	11	54	63	0	0	36	0.94
1106100--1106134	10	3.6	10	92	7	63	62	0	0	37	0.95
1106260--1106292	15	2.3	15	94	5	59	42	0	0	57	0.98
1106263--1106301	15	2.4	17	83	12	55	46	0	0	53	1.00
1106261--1106301	14	2.6	16	88	11	59	43	0	0	56	0.99
1106621--1106654	15	2.2	16	89	5	52	58	0	2	38	1.13
1108908--1108933	11	2.4	11	100	0	52	92	7	0	0	0.39
1114574--1114671	14	6.3	15	69	18	51	75	1	9	14	1.09
1114635--1114672	20	1.9	19	89	5	58	76	0	7	15	1.01
1115777--1115833	21	2.7	21	81	8	62	71	0	3	24	1.01
1115790--1115874	31	2.7	30	84	13	102	69	0	1	29	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1115802--1115875	18	4.4	17	69	20	57	68	0	1	29	0.97
1115868--1116068	38	5.2	38	77	13	126	46	6	2	43	1.45
1116031--1116087	28	2.1	27	90	3	87	43	5	1	49	1.35
1116033--1116092	25	2.3	26	85	8	77	48	6	1	43	1.39
1116059--1116195	37	4.0	34	84	13	183	47	8	0	43	1.39
1116113--1116184	30	2.4	30	93	6	119	47	8	0	44	1.33
1115950--1116195	103	2.4	102	83	11	299	45	7	2	44	1.43
1116056--1116195	67	2.0	69	89	9	214	47	8	0	42	1.39
1117986--1118016	16	1.9	16	100	0	62	58	3	0	38	1.15
1120345--1120499	77	2.0	77	96	0	283	31	17	20	30	1.95

Tables:   1   2   3   4   5